{ "Cut1": { "tool_id": [ [ "Cut1", "Cut1" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/ewas-suite", "Infinium Human Methylation BeadChip", "Epigenetics", "/topics/epigenetics/tutorials/ewas-suite/tutorial.html" ], [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "genome-annotation/bacterial-comparative-genomics-dataset-construction", "Dataset construction for bacterial comparative genomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ], [ "single-cell/GO-enrichment", "GO Enrichment Analysis on Single-Cell RNA-Seq Data", "Single Cell", "/topics/single-cell/tutorials/GO-enrichment/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ], [ "single-cell/scrna-case_alevin-combine-datasets", "Combining single cell datasets after pre-processing", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ], [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "statistics/gpu_jupyter_lab", "A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy", "Statistics and machine learning", "/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/network-analysis-with-heinz", "Network analysis with Heinz", "Transcriptomics", "/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ], [ "variant-analysis/countess-mave-chek2", "Calculating CHEK2 variant effect scores from MAVE data with CountESS", "Variant Analysis", "/topics/variant-analysis/tutorials/countess-mave-chek2/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "visualisation/circos", "Visualisation with Circos", "Visualisation", "/topics/visualisation/tutorials/circos/tutorial.html" ], [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "Filter1": { "tool_id": [ [ "Filter1", "Filter1" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ], [ "ecology/gbif_cleaning", "Cleaning GBIF data for the use in Ecology", "Ecology", "/topics/ecology/tutorials/gbif_cleaning/tutorial.html" ], [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ], [ "ecology/species-distribution-modeling", "Species distribution modeling", "Ecology", "/topics/ecology/tutorials/species-distribution-modeling/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "introduction/galaxy-intro-strands", "Introduction to Genomics and Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html" ], [ "metabolomics/msi-analyte-distribution", "Mass spectrometry imaging: Examining the spatial distribution of analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html" ], [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ], [ "microbiome/beer-data-analysis", "Identification of the micro-organisms in a beer using Nanopore sequencing", "Microbiome", "/topics/microbiome/tutorials/beer-data-analysis/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "proteomics/DIA_Analysis_MSstats", "Statistical analysis of DIA data", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html" ], [ "proteomics/DIA_lib_OSW", "Library Generation for DIA Analysis", "Proteomics", "/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/multiGSEA-tutorial", "Multiomics data analysis using MultiGSEA", "Proteomics", "/topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html" ], [ "proteomics/neoantigen-hla-binding-novel-peptides", "Neoantigen 5b: IEDB binding Validated Neopeptides", "Proteomics", "/topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ], [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ], [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "statistics/gpu_jupyter_lab", "A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy", "Statistics and machine learning", "/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/goenrichment", "GO Enrichment Analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/goenrichment/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ], [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ], [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ], [ "variant-analysis/sars-cov-2-variant-discovery", "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "devteam/fastqc/fastqc": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1", "0.74+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0", "0.74+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0", "0.73+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1", "0.72+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72", "0.72" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71", "0.71" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69", "0.69" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68", "0.68" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65", "0.65" ] ], "tutorials": [ [ "assembly/general-introduction", "An Introduction to Genome Assembly", "Assembly", "/topics/assembly/tutorials/general-introduction/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "assembly/unicycler-assembly", "Unicycler Assembly", "Assembly", "/topics/assembly/tutorials/unicycler-assembly/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "ecology/de-novo-rad-seq", "RAD-Seq de-novo data analysis", "Ecology", "/topics/ecology/tutorials/de-novo-rad-seq/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ], [ "introduction/galaxy-intro-short", "A short introduction to Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-short/tutorial.html" ], [ "microbiome/beer-data-analysis", "Identification of the micro-organisms in a beer using Nanopore sequencing", "Microbiome", "/topics/microbiome/tutorials/beer-data-analysis/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ], [ "sequence-analysis/quality-control", "Quality Control", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-control/tutorial.html" ], [ "sequence-analysis/sars-with-galaxy-on-anvil", "SARS-CoV-2 Viral Sample Alignment and Variant Visualization", "Sequence analysis", "/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html" ], [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ], [ "single-cell/scrna-umis", "Understanding Barcodes", "Single Cell", "/topics/single-cell/tutorials/scrna-umis/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ], [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ], [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "Grep1": { "tool_id": [ [ "Grep1", "Grep1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ], [ "digital-humanities/grobid", "Text-Mining articles with GROBID", "Digital Humanities", "/topics/digital-humanities/tutorials/grobid/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "genome-annotation/amr-gene-detection", "Identification of AMR genes in an assembled bacterial genome", "Genome Annotation", "/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "microbiome/clinical-mp-5-data-interpretation", "Clinical Metaproteomics 5: Data Interpretation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-5-data-interpretation/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/DIA_Analysis_MSstats", "Statistical analysis of DIA data", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html" ], [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "proteomics/clinical-mp-5-data-interpretation", "Clinical Metaproteomics 5: Data Interpretation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html" ], [ "proteomics/mass-spectrometry-imaging-loading-exploring-data", "Mass spectrometry imaging: Loading and exploring MSI data", "Proteomics", "/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ], [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-id-sg-ps", "Peptide and Protein ID using SearchGUI and PeptideShaker", "Proteomics", "/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "visualisation/circos", "Visualisation with Circos", "Visualisation", "/topics/visualisation/tutorials/circos/tutorial.html" ] ] }, "iuc/multiqc/multiqc": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1", "1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9", "1.9" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1", "1.8+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0", "1.8+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7", "1.7" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6", "1.6" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0", "1.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0", "1.33+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4", "1.27+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3", "1.27+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0", "1.27+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0", "1.2.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", "1.11+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0", "1.11+galaxy0" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/general-introduction", "An Introduction to Genome Assembly", "Assembly", "/topics/assembly/tutorials/general-introduction/tutorial.html" ], [ "assembly/hybrid_denovo_assembly", "Hybrid genome assembly - Nanopore and Illumina", "Assembly", "/topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/unicycler-assembly", "Unicycler Assembly", "Assembly", "/topics/assembly/tutorials/unicycler-assembly/tutorial.html" ], [ "contributing/create-new-tutorial-content", "Creating content in Markdown", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html" ], [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "galaxy-interface/workflow-fairification", "Annotate, prepare tests and publish Galaxy workflows in workflow registries", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html" ], [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "introduction/vsi_qc", "Very Short Introductions: QC", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/vsi_qc/tutorial.html" ], [ "microbiome/host-removal", "Remove contamination and host reads", "Microbiome", "/topics/microbiome/tutorials/host-removal/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ], [ "sequence-analysis/quality-control", "Quality Control", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-control/tutorial.html" ], [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "single-cell/scrna-preprocessing-tenx", "Pre-processing of 10X Single-Cell RNA Datasets", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "Remove beginning1": { "tool_id": [ [ "Remove beginning1", "Remove beginning1" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "digital-humanities/introduction_to_dh", "Introduction to Digital Humanities in Galaxy", "Digital Humanities", "/topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ], [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ], [ "epigenetics/ewas-suite", "Infinium Human Methylation BeadChip", "Epigenetics", "/topics/epigenetics/tutorials/ewas-suite/tutorial.html" ], [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "genome-annotation/bacterial-comparative-genomics-dataset-construction", "Dataset construction for bacterial comparative genomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html" ], [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ], [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ], [ "statistics/regression_machinelearning", "Regression in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/regression_machinelearning/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "visualisation/circos", "Visualisation with Circos", "Visualisation", "/topics/visualisation/tutorials/circos/tutorial.html" ] ] }, "upload1": { "tool_id": [ [ "upload1", "upload1" ] ], "tutorials": [ [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "assembly/mrsa-illumina", "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data", "Assembly", "/topics/assembly/tutorials/mrsa-illumina/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "contributing/create-new-tutorial-content", "Creating content in Markdown", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial-content/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/bacterial-isolate-species-contamination-checking", "Checking expected species and contamination in bacterial isolate", "Ecology", "/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html" ], [ "evolution/bacterial-comparative-genomics", "Phylogenetic analysis for bacterial comparative genomics", "Evolution", "/topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html" ], [ "evolution/mtb_phylogeny", "Tree thinking for tuberculosis evolution and epidemiology", "Evolution", "/topics/evolution/tutorials/mtb_phylogeny/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "genome-annotation/amr-gene-detection", "Identification of AMR genes in an assembled bacterial genome", "Genome Annotation", "/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html" ], [ "genome-annotation/bacterial-comparative-genomics-dataset-construction", "Dataset construction for bacterial comparative genomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html" ], [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ], [ "genome-annotation/bacterial-genome-quality-control", "Bacterial genome quality control", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html" ], [ "genome-annotation/bacterial-pangenomics", "Bacterial pangenomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html" ], [ "genome-annotation/pangenome-annotation-with-roary", "Pangenome analysis with Roary", "Genome Annotation", "/topics/genome-annotation/tutorials/pangenome-annotation-with-roary/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-101", "Galaxy Basics for genomics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "sequence-analysis/quality-contamination-control", "Quality and contamination control in bacterial isolate using Illumina MiSeq Data", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/sars-cov-2-variant-discovery", "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ], [ "visualisation/circos", "Visualisation with Circos", "Visualisation", "/topics/visualisation/tutorials/circos/tutorial.html" ] ] }, "nml/collapse_collections/collapse_dataset": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0", "5.1.0" ], [ "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2", "4.2" ], [ "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0", "4.0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ], [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "galaxy-interface/collections", "Using dataset collections", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/collections/tutorial.html" ], [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ], [ "imaging/hela-screen-analysis", "Analyse HeLa fluorescence siRNA screen", "Imaging", "/topics/imaging/tutorials/hela-screen-analysis/tutorial.html" ], [ "imaging/parameter-tuning", "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy", "Imaging", "/topics/imaging/tutorials/parameter-tuning/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ] ] }, "bgruening/text_processing/tp_sort_header_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy0", "9.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", "1.1.1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-101", "Galaxy Basics for genomics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "introduction/galaxy-intro-strands", "Introduction to Genomics and Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "proteomics/mass-spectrometry-imaging-loading-exploring-data", "Mass spectrometry imaging: Loading and exploring MSI data", "Proteomics", "/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "statistics/flexynesis_cbio_import", "Prepare Data from CbioPortal for Flexynesis Integration", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ], [ "transcriptomics/small_ncrna_clustering", "Small Non-coding RNA Clustering using BlockClust", "Transcriptomics", "/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html" ] ] }, "bgruening/text_processing/tp_cut_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2", "9.3+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy0", "9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0", "1.1.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0", "1.0.0" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ], [ "ecology/obisindicators", "Obis marine indicators", "Ecology", "/topics/ecology/tutorials/obisindicators/tutorial.html" ], [ "ecology/species-distribution-modeling", "Species distribution modeling", "Ecology", "/topics/ecology/tutorials/species-distribution-modeling/tutorial.html" ], [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "statistics/flexynesis_cbio_import", "Prepare Data from CbioPortal for Flexynesis Integration", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "statistics/fruit_360", "Image classification in Galaxy with fruit 360 dataset", "Statistics and machine learning", "/topics/statistics/tutorials/fruit_360/tutorial.html" ], [ "transcriptomics/rna-seq-counts-to-genes", "2: RNA-seq counts to genes", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html" ], [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "devteam/column_maker/Add_a_column1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1+galaxy0", "2.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1", "2.1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0", "2.0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6", "1.6" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.4", "1.4" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0", "1.3.0" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "introduction/galaxy-intro-rdm", "Introduction to Galaxy as an RDM platform", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html" ], [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "statistics/flexynesis_survival", "Identifing Survival Markers of Brain tumor with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_survival/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "bgruening/text_processing/tp_cat": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/1.0.0", "1.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1", "0.1.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0", "0.1.0" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "computational-chemistry/zauberkugel", "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib", "Computational chemistry", "/topics/computational-chemistry/tutorials/zauberkugel/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "galaxy-interface/ncbi-sarf", "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html" ], [ "genome-annotation/lncrna", "Long non-coding RNAs (lncRNAs) annotation with FEELnc", "Genome Annotation", "/topics/genome-annotation/tutorials/lncrna/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-strands", "Introduction to Genomics and Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html" ], [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "__EXTRACT_DATASET__": { "tool_id": [ [ "__EXTRACT_DATASET__", "__EXTRACT_DATASET__" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "climate/fates", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", "Earth Data science", "/topics/climate/tutorials/fates/tutorial.html" ], [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/biapy", "Execute a BiaPy workflow in Galaxy", "Imaging", "/topics/imaging/tutorials/biapy/tutorial.html" ], [ "imaging/electrophoresis-gel-bands-image-analysis", "Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools", "Imaging", "/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html" ], [ "imaging/iscc-suite", "Content Tracking and Verification in Galaxy Workflows with ISCC-SUM", "Imaging", "/topics/imaging/tutorials/iscc-suite/tutorial.html" ], [ "imaging/process-image-bioimageio", "Using BioImage.IO models for image analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/process-image-bioimageio/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "statistics/flexynesis_cbio_import", "Prepare Data from CbioPortal for Flexynesis Integration", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "statistics/flexynesis_survival", "Identifing Survival Markers of Brain tumor with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_survival/tutorial.html" ], [ "statistics/flexynesis_unsupervised", "Unsupervised Analysis of Bone Marrow Cells with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_unsupervised/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ] ] }, "Grouping1": { "tool_id": [ [ "Grouping1", "Grouping1" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/bioconductor-scp", "Single Cell Proteomics data analysis with bioconductor-scp", "Proteomics", "/topics/proteomics/tutorials/bioconductor-scp/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ] ] }, "join1": { "tool_id": [ [ "join1", "join1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ], [ "variant-analysis/countess-mave-chek2", "Calculating CHEK2 variant effect scores from MAVE data with CountESS", "Variant Analysis", "/topics/variant-analysis/tutorials/countess-mave-chek2/tutorial.html" ] ] }, "cat1": { "tool_id": [ [ "cat1", "cat1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "genome-annotation/bacterial-comparative-genomics-dataset-construction", "Dataset construction for bacterial comparative genomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-strands", "Introduction to Genomics and Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html" ], [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ] ] }, "iuc/query_tabular/query_tabular": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2", "3.3.2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.1", "3.3.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0", "3.3.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0", "3.0.0" ] ], "tutorials": [ [ "galaxy-interface/ncbi-sarf", "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/metaproteomics", "Metaproteomics tutorial", "Proteomics", "/topics/proteomics/tutorials/metaproteomics/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ], [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ], [ "proteomics/neoantigen-peptide-verification", "Neoantigen 3: PepQuery2 Verification", "Proteomics", "/topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html" ], [ "proteomics/neoantigen-predicting-hla-binding", "Neoantigen 5a: Predicting HLA Binding", "Proteomics", "/topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html" ], [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "proteomics/proteogenomics-dbsearch", "Proteogenomics 2: Database Search", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" ], [ "proteomics/proteogenomics-novel-peptide-analysis", "Proteogenomics 3: Novel peptide analysis", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html" ], [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ] ] }, "galaxyp/regex_find_replace/regexColumn1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3", "1.0.3" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.2", "1.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1", "1.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0", "1.0.0" ] ], "tutorials": [ [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ], [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/fastp/fastp": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3", "1.0.1+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.1+galaxy0", "0.24.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4", "0.24.0+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1", "0.23.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0", "0.23.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0", "0.23.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0", "0.20.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1", "0.19.5+galaxy1" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/mrsa-illumina", "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data", "Assembly", "/topics/assembly/tutorials/mrsa-illumina/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "ecology/eDNA-taxonomic-analysis", "Taxonomic Analysis of eDNA", "Ecology", "/topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html" ], [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "introduction/vsi_qc", "Very Short Introductions: QC", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/vsi_qc/tutorial.html" ], [ "microbiome/beer-data-analysis", "Identification of the micro-organisms in a beer using Nanopore sequencing", "Microbiome", "/topics/microbiome/tutorials/beer-data-analysis/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "sequence-analysis/quality-contamination-control", "Quality and contamination control in bacterial isolate using Illumina MiSeq Data", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "bgruening/text_processing/tp_replace_in_line": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2", "1.1.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1", "1.1.1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "digital-humanities/introduction_to_dh", "Introduction to Digital Humanities in Galaxy", "Digital Humanities", "/topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ], [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ], [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ], [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-counts-to-genes", "2: RNA-seq counts to genes", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ] ] }, "iuc/jbrowse/jbrowse": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0", "1.16.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1", "1.16.8+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3", "1.16.4+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "1.16.11+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0", "1.16.11+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0", "1.16.10+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3", "0.7.0.3" ] ], "tutorials": [ [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "genome-annotation/amr-gene-detection", "Identification of AMR genes in an assembled bacterial genome", "Genome Annotation", "/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html" ], [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ], [ "genome-annotation/annotation-with-maker-short", "Genome annotation with Maker (short)", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html" ], [ "genome-annotation/annotation-with-prokka", "Genome annotation with Prokka", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html" ], [ "genome-annotation/apollo", "Refining Genome Annotations with Apollo (prokaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo/tutorial.html" ], [ "genome-annotation/apollo-euk", "Refining Genome Annotations with Apollo (eukaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo-euk/tutorial.html" ], [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ], [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ], [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ], [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ], [ "genome-annotation/helixer", "Genome annotation with Helixer", "Genome Annotation", "/topics/genome-annotation/tutorials/helixer/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ], [ "sequence-analysis/sars-with-galaxy-on-anvil", "SARS-CoV-2 Viral Sample Alignment and Variant Visualization", "Sequence analysis", "/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html" ], [ "variant-analysis/microbial-variants", "Microbial Variant Calling", "Variant Analysis", "/topics/variant-analysis/tutorials/microbial-variants/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ], [ "visualisation/jbrowse", "Genomic Data Visualisation with JBrowse", "Visualisation", "/topics/visualisation/tutorials/jbrowse/tutorial.html" ] ] }, "bgruening/text_processing/tp_awk_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0", "9.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "1.1.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1", "1.1.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0", "1.1.0" ] ], "tutorials": [ [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ], [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ], [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ], [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ], [ "genome-annotation/hpc-for-lsgc", "From small to large-scale genome comparison", "Genome Annotation", "/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html" ], [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ], [ "proteomics/neoantigen-predicting-hla-binding", "Neoantigen 5a: Predicting HLA Binding", "Proteomics", "/topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "devteam/bwa/bwa_mem": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19", "0.7.19" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18", "0.7.18" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2", "0.7.17.2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1", "0.7.17.1" ] ], "tutorials": [ [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/hybrid_denovo_assembly", "Hybrid genome assembly - Nanopore and Illumina", "Assembly", "/topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html" ], [ "galaxy-interface/collections", "Using dataset collections", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/collections/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ], [ "sequence-analysis/sars-with-galaxy-on-anvil", "SARS-CoV-2 Viral Sample Alignment and Variant Visualization", "Sequence analysis", "/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html" ], [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ], [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "iuc/datamash_ops/datamash_ops": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.9+galaxy0", "1.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0", "1.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0", "1.8+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2", "1.1.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0", "1.1.0" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ], [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-101", "Galaxy Basics for genomics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "statistics/flexynesis_survival", "Identifing Survival Markers of Brain tumor with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_survival/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/sars-cov-2-variant-discovery", "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html" ] ] }, "lparsons/cutadapt/cutadapt": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2", "5.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy0", "5.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0", "5.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0", "5.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "4.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0", "4.8+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", "4.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", "4.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0", "4.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2", "3.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy0", "3.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy1", "3.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5", "1.16.5" ], [ "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3", "1.16.3" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "sequence-analysis/quality-control", "Quality Control", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-control/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ] ] }, "imgteam/unzip/unzip": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy5", "6.0+galaxy5" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy3", "6.0+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy2", "6.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0", "6.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2", "0.2" ] ], "tutorials": [ [ "digital-humanities/mfa_tutorial", "Montreal Forced Aligner", "Digital Humanities", "/topics/digital-humanities/tutorials/mfa_tutorial/tutorial.html" ], [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ], [ "ecology/yolo_predict_deepsea", "Object detection with YOLO", "Ecology", "/topics/ecology/tutorials/yolo_predict_deepsea/tutorial.html" ], [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/hela-screen-analysis", "Analyse HeLa fluorescence siRNA screen", "Imaging", "/topics/imaging/tutorials/hela-screen-analysis/tutorial.html" ], [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ], [ "imaging/yolo-segmentation-training", "Training Custom YOLO Models for Segmentation of Bioimages", "Imaging", "/topics/imaging/tutorials/yolo-segmentation-training/tutorial.html" ], [ "introduction/galaxy-intro-rdm", "Introduction to Galaxy as an RDM platform", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ] ] }, "bgruening/text_processing/tp_replace_in_column": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0", "9.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0", "9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3", "1.1.3" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "single-cell/scrna-case_alevin-combine-datasets", "Combining single cell datasets after pre-processing", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ], [ "statistics/flexynesis_survival", "Identifing Survival Markers of Brain tumor with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_survival/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ] ] }, "iuc/anndata_inspect/anndata_inspect": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "0.7.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.11.4+galaxy3", "0.11.4+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1", "0.10.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0", "0.10.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0", "0.10.3+galaxy0" ] ], "tutorials": [ [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ], [ "single-cell/scrna-case_alevin-combine-datasets", "Combining single cell datasets after pre-processing", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "bgruening/text_processing/tp_find_and_replace": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0", "9.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", "1.1.4" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3", "1.1.3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.2", "1.1.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1", "1.1.1" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "climate/fates", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", "Earth Data science", "/topics/climate/tutorials/fates/tutorial.html" ], [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "digital-humanities/Whisper_speech_recognition", "Transcribing Audio and Video files with Automated Speech Recognition", "Digital Humanities", "/topics/digital-humanities/tutorials/Whisper_speech_recognition/tutorial.html" ], [ "digital-humanities/introduction_to_dh", "Introduction to Digital Humanities in Galaxy", "Digital Humanities", "/topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html" ], [ "ecology/species-distribution-modeling", "Species distribution modeling", "Ecology", "/topics/ecology/tutorials/species-distribution-modeling/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ] ] }, "bgruening/text_processing/tp_grep_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0", "9.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1", "1.1.1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/md-simulation-gromacs", "Running molecular dynamics simulations using GROMACS", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html" ], [ "digital-humanities/Whisper_speech_recognition", "Transcribing Audio and Video files with Automated Speech Recognition", "Digital Humanities", "/topics/digital-humanities/tutorials/Whisper_speech_recognition/tutorial.html" ], [ "digital-humanities/introduction_to_dh", "Introduction to Digital Humanities in Galaxy", "Digital Humanities", "/topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "proteomics/multiGSEA-tutorial", "Multiomics data analysis using MultiGSEA", "Proteomics", "/topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html" ], [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/busco/busco": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy2", "5.8.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1", "5.8.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0", "5.8.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0", "5.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "5.5.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0", "5.4.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0", "5.4.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0", "5.3.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2", "5.2.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4", "4.1.4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1", "3.0.2+galaxy1" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-quality-control", "Genome Assembly Quality Control", "Assembly", "/topics/assembly/tutorials/assembly-quality-control/tutorial.html" ], [ "assembly/hifi-assembly", "Genome assembly using PacBio data", "Assembly", "/topics/assembly/tutorials/hifi-assembly/tutorial.html" ], [ "assembly/hybrid_denovo_assembly", "Hybrid genome assembly - Nanopore and Illumina", "Assembly", "/topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ], [ "genome-annotation/annotation-with-maker-short", "Genome annotation with Maker (short)", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html" ], [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ], [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ], [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ], [ "genome-annotation/helixer", "Genome annotation with Helixer", "Genome Annotation", "/topics/genome-annotation/tutorials/helixer/tutorial.html" ] ] }, "devteam/bowtie2/bowtie2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0", "2.5.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1", "2.5.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1", "2.4.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0", "2.4.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0", "2.3.4.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3", "2.3.4.3" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2", "2.3.2.2" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ], [ "genome-annotation/amr-gene-detection", "Identification of AMR genes in an assembled bacterial genome", "Genome Annotation", "/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html" ], [ "microbiome/host-removal", "Remove contamination and host reads", "Microbiome", "/topics/microbiome/tutorials/host-removal/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ] ] }, "iuc/falco/falco": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0", "1.2.4+galaxy0" ] ], "tutorials": [ [ "assembly/mrsa-illumina", "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data", "Assembly", "/topics/assembly/tutorials/mrsa-illumina/tutorial.html" ], [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ], [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "galaxy-interface/workflow-fairification", "Annotate, prepare tests and publish Galaxy workflows in workflow registries", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html" ], [ "sequence-analysis/quality-contamination-control", "Quality and contamination control in bacterial isolate using Illumina MiSeq Data", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html" ], [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "galaxyp/regex_find_replace/regex1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3", "1.0.3" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2", "1.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1", "1.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0", "1.0.0" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "ecology/marine_omics_bgc", "Marine Omics identifying biosynthetic gene clusters", "Ecology", "/topics/ecology/tutorials/marine_omics_bgc/tutorial.html" ], [ "ecology/openrefine_gbif", "Cleaning GBIF data using OpenRefine", "Ecology", "/topics/ecology/tutorials/openrefine_gbif/tutorial.html" ], [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "bgruening/text_processing/tp_easyjoin_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy0", "9.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", "1.1.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1", "1.1.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0", "1.0.0" ] ], "tutorials": [ [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "iuc/quast/quast": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0", "5.3.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1", "5.2.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0", "5.2.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4", "5.0.2+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3", "5.0.2+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0", "5.0.2+galaxy0" ] ], "tutorials": [ [ "assembly/assembly-quality-control", "Genome Assembly Quality Control", "Assembly", "/topics/assembly/tutorials/assembly-quality-control/tutorial.html" ], [ "assembly/general-introduction", "An Introduction to Genome Assembly", "Assembly", "/topics/assembly/tutorials/general-introduction/tutorial.html" ], [ "assembly/hifi-assembly", "Genome assembly using PacBio data", "Assembly", "/topics/assembly/tutorials/hifi-assembly/tutorial.html" ], [ "assembly/hybrid_denovo_assembly", "Hybrid genome assembly - Nanopore and Illumina", "Assembly", "/topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "assembly/mrsa-illumina", "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data", "Assembly", "/topics/assembly/tutorials/mrsa-illumina/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "assembly/unicycler-assembly", "Unicycler Assembly", "Assembly", "/topics/assembly/tutorials/unicycler-assembly/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "assembly/vgp_workflow_training", "Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data", "Assembly", "/topics/assembly/tutorials/vgp_workflow_training/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "iuc/anndata_manipulate/anndata_manipulate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1", "0.7.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0", "0.7.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1", "0.10.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0", "0.10.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0", "0.10.3+galaxy0" ] ], "tutorials": [ [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ], [ "single-cell/scrna-case_alevin-combine-datasets", "Combining single cell datasets after pre-processing", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ], [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ] ] }, "galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0", "1.2.0" ] ], "tutorials": [ [ "microbiome/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/database-handling", "Protein FASTA Database Handling", "Proteomics", "/topics/proteomics/tutorials/database-handling/tutorial.html" ], [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ], [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "devteam/tabular_to_fasta/tab2fasta": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1", "1.1.1" ] ], "tutorials": [ [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/database-handling", "Protein FASTA Database Handling", "Proteomics", "/topics/proteomics/tutorials/database-handling/tutorial.html" ], [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ], [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/neoantigen-peptide-verification", "Neoantigen 3: PepQuery2 Verification", "Proteomics", "/topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html" ], [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "proteomics/proteogenomics-dbsearch", "Proteogenomics 2: Database Search", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "iuc/bandage/bandage_image": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4", "2022.09+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4", "0.8.1+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2", "0.8.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0", "0.8.1+galaxy0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/debruijn-graph-assembly", "De Bruijn Graph Assembly", "Assembly", "/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "assembly/mrsa-illumina", "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data", "Assembly", "/topics/assembly/tutorials/mrsa-illumina/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "bgruening/text_processing/tp_sorted_uniq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", "1.1.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0", "1.0.0" ] ], "tutorials": [ [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ], [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ] ] }, "bgruening/text_processing/tp_sed_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1", "1.1.1" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/ggplot2_point/ggplot2_point": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2", "3.5.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "3.4.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0", "3.3.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2", "2.2.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1", "2.2.1+galaxy1" ] ], "tutorials": [ [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ], [ "climate/fates", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", "Earth Data science", "/topics/climate/tutorials/fates/tutorial.html" ], [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ], [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "statistics/clustering_machinelearning", "Clustering in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/clustering_machinelearning/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ], [ "variant-analysis/countess-mave-chek2", "Calculating CHEK2 variant effect scores from MAVE data with CountESS", "Variant Analysis", "/topics/variant-analysis/tutorials/countess-mave-chek2/tutorial.html" ] ] }, "Count1": { "tool_id": [ [ "Count1", "Count1" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "ecology/eDNA-taxonomic-analysis", "Taxonomic Analysis of eDNA", "Ecology", "/topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html" ], [ "ecology/gbif_cleaning", "Cleaning GBIF data for the use in Ecology", "Ecology", "/topics/ecology/tutorials/gbif_cleaning/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/collection_column_join/collection_column_join": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3", "0.0.3" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ] ] }, "sort1": { "tool_id": [ [ "sort1", "sort1" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "computational-chemistry/zauberkugel", "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib", "Computational chemistry", "/topics/computational-chemistry/tutorials/zauberkugel/tutorial.html" ], [ "genome-annotation/bacterial-comparative-genomics-dataset-construction", "Dataset construction for bacterial comparative genomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ] ] }, "iuc/table_compute/table_compute": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy2", "1.2.4+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy1", "1.2.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "1.2.4+galaxy0" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/neoantigen-hla-binding-novel-peptides", "Neoantigen 5b: IEDB binding Validated Neopeptides", "Proteomics", "/topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "statistics/flexynesis_cbio_import", "Prepare Data from CbioPortal for Flexynesis Integration", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ] ] }, "imgteam/2d_auto_threshold/ip_threshold": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.25.2+galaxy0", "0.25.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.25.0+galaxy0", "0.25.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3", "0.18.1+galaxy3" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/hela-screen-analysis", "Analyse HeLa fluorescence siRNA screen", "Imaging", "/topics/imaging/tutorials/hela-screen-analysis/tutorial.html" ], [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/iscc-suite", "Content Tracking and Verification in Galaxy Workflows with ISCC-SUM", "Imaging", "/topics/imaging/tutorials/iscc-suite/tutorial.html" ], [ "imaging/parameter-tuning", "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy", "Imaging", "/topics/imaging/tutorials/parameter-tuning/tutorial.html" ], [ "imaging/process-image-bioimageio", "Using BioImage.IO models for image analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/process-image-bioimageio/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "iuc/datamash_transpose/datamash_transpose": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.9+galaxy0", "1.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1", "1.8+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy0", "1.8+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2", "1.1.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0", "1.1.0" ] ], "tutorials": [ [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ] ] }, "Show beginning1": { "tool_id": [ [ "Show beginning1", "Show beginning1" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "galaxy-interface/workflow-editor", "Creating, Editing and Importing Galaxy Workflows", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ] ] }, "param_value_from_file": { "tool_id": [ [ "param_value_from_file", "param_value_from_file" ] ], "tutorials": [ [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/iscc-suite", "Content Tracking and Verification in Galaxy Workflows with ISCC-SUM", "Imaging", "/topics/imaging/tutorials/iscc-suite/tutorial.html" ], [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ], [ "imaging/parameter-tuning", "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy", "Imaging", "/topics/imaging/tutorials/parameter-tuning/tutorial.html" ], [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "pjbriggs/trimmomatic/trimmomatic": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2", "0.39+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0", "0.39+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1", "0.38.1" ], [ "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0", "0.38.0" ], [ "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5", "0.36.5" ], [ "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", "0.32.3" ] ], "tutorials": [ [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "iuc/collection_element_identifiers/collection_element_identifiers": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3", "0.0.3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", "0.0.2" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ], [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "__FLATTEN__": { "tool_id": [ [ "__FLATTEN__", "__FLATTEN__" ] ], "tutorials": [ [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ], [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "crs4/taxonomy_krona_chart/taxonomy_krona_chart": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0", "2.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1", "2.7.1" ], [ "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1", "2.6.1.1" ], [ "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1", "2.6.1" ] ], "tutorials": [ [ "microbiome/beer-data-analysis", "Identification of the micro-organisms in a beer using Nanopore sequencing", "Microbiome", "/topics/microbiome/tutorials/beer-data-analysis/tutorial.html" ], [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ] ] }, "Paste1": { "tool_id": [ [ "Paste1", "Paste1" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ], [ "galaxy-interface/workflow-editor", "Creating, Editing and Importing Galaxy Workflows", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/scrna-case_alevin-combine-datasets", "Combining single cell datasets after pre-processing", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ] ] }, "interactive_tool_rstudio": { "tool_id": [ [ "interactive_tool_rstudio", "interactive_tool_rstudio" ] ], "tutorials": [ [ "data-science/bash-git", "Version Control with Git", "Foundations of Data Science", "/topics/data-science/tutorials/bash-git/tutorial.html" ], [ "data-science/r-advanced", "Advanced R in Galaxy", "Foundations of Data Science", "/topics/data-science/tutorials/r-advanced/tutorial.html" ], [ "data-science/r-basics", "R basics in Galaxy", "Foundations of Data Science", "/topics/data-science/tutorials/r-basics/tutorial.html" ], [ "evolution/mtb_phylogeny", "Tree thinking for tuberculosis evolution and epidemiology", "Evolution", "/topics/evolution/tutorials/mtb_phylogeny/tutorial.html" ], [ "galaxy-interface/rstudio", "RStudio in Galaxy", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/rstudio/tutorial.html" ], [ "statistics/intro-to-ml-with-r", "Introduction to Machine Learning using R", "Statistics and machine learning", "/topics/statistics/tutorials/intro-to-ml-with-r/tutorial.html" ], [ "transcriptomics/rna-seq-counts-to-viz-in-r", "RNA Seq Counts to Viz in R", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-volcanoplot-r", "Visualization of RNA-Seq results with Volcano Plot in R", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html" ] ] }, "galaxyp/maxquant/maxquant": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0", "2.0.3.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy4", "1.6.17.0+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2", "1.6.17.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3", "1.6.10.43+galaxy3" ] ], "tutorials": [ [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "proteomics/DIA_lib_OSW", "Library Generation for DIA Analysis", "Proteomics", "/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-4-quantitation", "Clinical Metaproteomics 4: Quantitation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/maxquant-msstats-tmt", "MaxQuant and MSstats for the analysis of TMT data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html" ] ] }, "iuc/filter_tabular/filter_tabular": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1", "3.3.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0", "3.3.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0", "2.0.0" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "galaxyp/msconvert/msconvert": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.6", "3.0.20287.6" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2", "3.0.20287.2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1", "3.0.19052.1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0", "3.0.19052.0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/encyclopedia", "EncyclopeDIA", "Proteomics", "/topics/proteomics/tutorials/encyclopedia/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/neoantigen-peptide-verification", "Neoantigen 3: PepQuery2 Verification", "Proteomics", "/topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html" ], [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ] ] }, "iuc/kraken2/kraken2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.17.1+galaxy0", "2.17.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2", "2.1.3+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1", "2.1.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1", "2.1.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0", "2.0.8_beta+galaxy0" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ], [ "ecology/bacterial-isolate-species-contamination-checking", "Checking expected species and contamination in bacterial isolate", "Ecology", "/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html" ], [ "microbiome/beer-data-analysis", "Identification of the micro-organisms in a beer using Nanopore sequencing", "Microbiome", "/topics/microbiome/tutorials/beer-data-analysis/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ], [ "sequence-analysis/quality-contamination-control", "Quality and contamination control in bacterial isolate using Illumina MiSeq Data", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/samtools_view/samtools_view": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy3", "1.9+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1", "1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1", "1.22+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0", "1.21+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "1.20+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0", "1.15.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2", "1.13+galaxy2" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ] ] }, "iuc/rgrnastar/rna_star": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1", "2.7.8a+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0", "2.7.8a+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.7a", "2.7.7a" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy0", "2.7.11b+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "2.7.11a+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0", "2.7.11a+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4", "2.7.10b+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3", "2.7.10b+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2", "2.5.2b-2" ] ], "tutorials": [ [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ], [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ], [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ], [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ], [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "imgteam/binary2labelimage/ip_binary_to_labelimage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.7.3+galaxy0", "0.7.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0", "0.5+galaxy0" ] ], "tutorials": [ [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/biapy", "Execute a BiaPy workflow in Galaxy", "Imaging", "/topics/imaging/tutorials/biapy/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/hela-screen-analysis", "Analyse HeLa fluorescence siRNA screen", "Imaging", "/topics/imaging/tutorials/hela-screen-analysis/tutorial.html" ], [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/process-image-bioimageio", "Using BioImage.IO models for image analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/process-image-bioimageio/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ] ] }, "iuc/scanpy_plot/scanpy_plot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3", "1.9.6+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "1.7.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0", "1.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.11.5+galaxy0", "1.11.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2", "1.10.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0", "1.10.2+galaxy0" ] ], "tutorials": [ [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "galaxyp/dbbuilder/dbbuilder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4", "0.3.4" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1", "0.3.1" ] ], "tutorials": [ [ "microbiome/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html" ], [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/database-handling", "Protein FASTA Database Handling", "Proteomics", "/topics/proteomics/tutorials/database-handling/tutorial.html" ] ] }, "devteam/fasta_to_tabular/fasta2tab": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1", "1.1.1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0", "1.1.0" ] ], "tutorials": [ [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/database-handling", "Protein FASTA Database Handling", "Proteomics", "/topics/proteomics/tutorials/database-handling/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "devteam/gffread/gffread": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.2.1.4+galaxy0", "2.2.2.1.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0", "2.2.1.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0", "2.2.1.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2", "2.2.1.2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1", "2.2.1.1" ] ], "tutorials": [ [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ], [ "genome-annotation/annotation-with-maker-short", "Genome annotation with Maker (short)", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html" ], [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ], [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ], [ "genome-annotation/helixer", "Genome annotation with Helixer", "Genome Annotation", "/topics/genome-annotation/tutorials/helixer/tutorial.html" ], [ "genome-annotation/lncrna", "Long non-coding RNAs (lncRNAs) annotation with FEELnc", "Genome Annotation", "/topics/genome-annotation/tutorials/lncrna/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/nanoplot/nanoplot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1", "1.42.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0", "1.41.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1", "1.28.2+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1", "1.25.0+galaxy1" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ], [ "sequence-analysis/quality-control", "Quality Control", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-control/tutorial.html" ] ] }, "iuc/minimap2/minimap2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0", "2.28+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0", "2.26+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0", "2.24+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4", "2.17+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2", "2.17+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1", "2.17+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17", "2.17" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "Summary_Statistics1": { "tool_id": [ [ "Summary_Statistics1", "Summary_Statistics1" ] ], "tutorials": [ [ "ecology/gbif_cleaning", "Cleaning GBIF data for the use in Ecology", "Ecology", "/topics/ecology/tutorials/gbif_cleaning/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "introduction/galaxy-intro-rdm", "Introduction to Galaxy as an RDM platform", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html" ], [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "devteam/samtools_stats/samtools_stats": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8", "2.0.8" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5", "2.0.5" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4", "2.0.4" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2", "2.0.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1", "2.0.1" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ], [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "bgruening/trim_galore/trim_galore": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy1", "0.6.7+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0", "0.6.7+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.10+galaxy0", "0.6.10+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", "0.4.3.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0", "0.4.3.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2", "0.4.2" ] ], "tutorials": [ [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ] ] }, "devteam/picard/picard_MarkDuplicates": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", "3.1.1.0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3", "2.18.2.3" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2", "2.18.2.2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1", "2.18.2.1" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "imgteam/overlay_images/ip_overlay_images": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.5", "0.0.5" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4", "0.0.4+galaxy4" ] ], "tutorials": [ [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/biapy", "Execute a BiaPy workflow in Galaxy", "Imaging", "/topics/imaging/tutorials/biapy/tutorial.html" ], [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/process-image-bioimageio", "Using BioImage.IO models for image analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/process-image-bioimageio/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "imgteam/2d_histogram_equalization/ip_histogram_equalization": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.25.2+galaxy0", "0.25.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0", "0.18.1+galaxy0" ] ], "tutorials": [ [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/parameter-tuning", "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy", "Imaging", "/topics/imaging/tutorials/parameter-tuning/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ], [ "imaging/yolo-segmentation-training", "Training Custom YOLO Models for Segmentation of Bioimages", "Imaging", "/topics/imaging/tutorials/yolo-segmentation-training/tutorial.html" ] ] }, "iuc/scanpy_inspect/scanpy_inspect": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3", "1.9.6+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0", "1.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.11.5+galaxy0", "1.11.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy2", "1.10.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1", "1.10.2+galaxy1" ] ], "tutorials": [ [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/scanpy_filter/scanpy_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3", "1.9.6+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0", "1.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.11.5+galaxy0", "1.11.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3", "1.10.2+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0", "1.10.2+galaxy0" ] ], "tutorials": [ [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "ebi-gxa/anndata_ops/anndata_ops": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0", "1.9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92", "1.8.1+galaxy92" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91", "1.8.1+galaxy91" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_alevin-combine-datasets", "Combining single cell datasets after pre-processing", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ] ] }, "bgruening/text_processing/tp_head_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.5+galaxy0", "9.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0", "1.1.0" ] ], "tutorials": [ [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "galaxy-interface/workflow-parameters", "Using Workflow Parameters", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html" ], [ "introduction/galaxy-intro-101", "Galaxy Basics for genomics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101/tutorial.html" ], [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ] ] }, "galaxyp/peptideshaker/search_gui": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy2", "4.0.41+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1", "4.0.41+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1", "3.3.10.1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/2.9.0", "2.9.0" ] ], "tutorials": [ [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/metaproteomics", "Metaproteomics tutorial", "Proteomics", "/topics/proteomics/tutorials/metaproteomics/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/protein-id-sg-ps", "Peptide and Protein ID using SearchGUI and PeptideShaker", "Proteomics", "/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html" ], [ "proteomics/proteogenomics-dbsearch", "Proteogenomics 2: Database Search", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" ] ] }, "galaxyp/peptideshaker/peptide_shaker": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy2", "2.0.33+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1", "2.0.33+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3", "1.16.36.3" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.11.0", "1.11.0" ] ], "tutorials": [ [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/metaproteomics", "Metaproteomics tutorial", "Proteomics", "/topics/proteomics/tutorials/metaproteomics/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ], [ "proteomics/protein-id-sg-ps", "Peptide and Protein ID using SearchGUI and PeptideShaker", "Proteomics", "/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html" ], [ "proteomics/proteogenomics-dbsearch", "Proteogenomics 2: Database Search", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" ] ] }, "bgruening/split_file_on_column/tp_split_on_column": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6", "0.6" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4", "0.4" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "imaging/parameter-tuning", "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy", "Imaging", "/topics/imaging/tutorials/parameter-tuning/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/GO-enrichment", "GO Enrichment Analysis on Single-Cell RNA-Seq Data", "Single Cell", "/topics/single-cell/tutorials/GO-enrichment/tutorial.html" ] ] }, "iuc/hisat2/hisat2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "2.2.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy0", "2.2.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5", "2.1.0+galaxy5" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3", "2.1.0+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3", "2.0.3" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ], [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ] ] }, "iuc/fasta_stats/fasta-stats": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0", "2.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1", "1.0.1" ] ], "tutorials": [ [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/debruijn-graph-assembly", "De Bruijn Graph Assembly", "Assembly", "/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html" ], [ "assembly/hifi-assembly", "Genome assembly using PacBio data", "Assembly", "/topics/assembly/tutorials/hifi-assembly/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ], [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ] ] }, "Convert characters1": { "tool_id": [ [ "Convert characters1", "Convert characters1" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ], [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ] ] }, "bgruening/flye/flye": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.6+galaxy0", "2.9.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.5+galaxy1", "2.9.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0", "2.9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0", "2.9.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0", "2.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "2.6" ] ], "tutorials": [ [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/hifi-assembly", "Genome assembly using PacBio data", "Assembly", "/topics/assembly/tutorials/hifi-assembly/tutorial.html" ], [ "assembly/hybrid_denovo_assembly", "Hybrid genome assembly - Nanopore and Illumina", "Assembly", "/topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "bgruening/split_file_to_collection/split_file_to_collection": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "0.5.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", "0.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0", "0.4.0" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ], [ "computational-chemistry/zauberkugel", "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib", "Computational chemistry", "/topics/computational-chemistry/tutorials/zauberkugel/tutorial.html" ], [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ], [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "sequence-analysis/viral_primer_design", "Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes", "Sequence analysis", "/topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html" ] ] }, "CONVERTER_gz_to_uncompressed": { "tool_id": [ [ "CONVERTER_gz_to_uncompressed", "CONVERTER_gz_to_uncompressed" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ], [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/sra_tools/fasterq_dump": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy1", "3.1.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1", "3.0.8+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.3+galaxy0", "3.0.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0", "2.11.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1", "2.10.7+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1", "2.10.4+galaxy1" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "galaxy-interface/ncbi-sarf", "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "rnateam/mafft/rbc_mafft": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+galaxy1", "7.526+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.526+galaxy0", "7.526+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0", "7.520+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.508+galaxy1", "7.508+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0", "7.489+galaxy0" ] ], "tutorials": [ [ "evolution/abc_intro_phylo", "Phylogenetics - Back to basics", "Evolution", "/topics/evolution/tutorials/abc_intro_phylo/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ], [ "sequence-analysis/viral_primer_design", "Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes", "Sequence analysis", "/topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "devteam/bamtools_filter/bamFilter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2", "2.5.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1", "2.4.1" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "sequence-analysis/mapping", "Mapping", "Sequence analysis", "/topics/sequence-analysis/tutorials/mapping/tutorial.html" ], [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "iuc/snpeff/snpEff": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1", "5.2+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0", "5.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2", "4.3+T.galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1", "4.3+T.galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0", "4.1.0" ] ], "tutorials": [ [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "variant-analysis/dip", "Calling variants in diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/dip/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "bgruening/openbabel_compound_convert/openbabel_compound_convert": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1", "3.1.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0", "3.1.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0", "2.4.2.2.0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ], [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/med-chem-data", "Data management in Medicinal Chemistry", "Computational chemistry", "/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html" ], [ "fair/med-chem-data", "Data management in Medicinal Chemistry", "FAIR Data, Workflows, and Research", "/topics/fair/tutorials/med-chem-data/tutorial.html" ], [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ] ] }, "iuc/macs2/macs2_callpeak": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0", "2.2.9.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0", "2.2.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6", "2.1.1.20160309.6" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.0", "2.1.1.20160309.0" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ] ] }, "bgruening/deeptools_compute_matrix/deeptools_compute_matrix": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.4+galaxy0", "3.5.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.5.1.0.0", "3.5.1.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0", "3.3.2.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ] ] }, "iuc/deseq2/deseq2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0", "2.11.40.8+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6", "2.11.40.6" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2", "2.11.40.2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39", "2.11.39" ] ], "tutorials": [ [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/network-analysis-with-heinz", "Network analysis with Heinz", "Transcriptomics", "/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ] ] }, "devteam/samtools_idxstats/samtools_idxstats": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.7", "2.0.7" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", "2.0.4" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3", "2.0.3" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2", "2.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.1", "2.0.1" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ] ] }, "__MERGE_COLLECTION__": { "tool_id": [ [ "__MERGE_COLLECTION__", "__MERGE_COLLECTION__" ] ], "tutorials": [ [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "bgruening/text_processing/tp_tail_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0", "1.1.0" ] ], "tutorials": [ [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ], [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "interactive_tool_panoply": { "tool_id": [ [ "interactive_tool_panoply", "interactive_tool_panoply" ] ], "tutorials": [ [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ], [ "climate/fates", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", "Earth Data science", "/topics/climate/tutorials/fates/tutorial.html" ], [ "climate/panoply", "Visualize Climate data with Panoply netCDF viewer", "Earth Data science", "/topics/climate/tutorials/panoply/tutorial.html" ], [ "climate/sentinel5_data", "Sentinel 5P data visualisation", "Earth Data science", "/topics/climate/tutorials/sentinel5_data/tutorial.html" ], [ "ecology/panoply_ebv", "Visualize EBV cube data with Panoply netCDF viewer", "Ecology", "/topics/ecology/tutorials/panoply_ebv/tutorial.html" ] ] }, "imgteam/2d_feature_extraction/ip_2d_feature_extraction": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.25.2+galaxy1", "0.25.2+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0", "0.18.1+galaxy0" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/electrophoresis-gel-bands-image-analysis", "Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools", "Imaging", "/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html" ], [ "imaging/hela-screen-analysis", "Analyse HeLa fluorescence siRNA screen", "Imaging", "/topics/imaging/tutorials/hela-screen-analysis/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ] ] }, "imgteam/split_image/ip_split_image": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/split_image/ip_split_image/2.3.5+galaxy1", "2.3.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/split_image/ip_split_image/2.3.5+galaxy0", "2.3.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/split_image/ip_split_image/2.2.3+galaxy1", "2.2.3+galaxy1" ] ], "tutorials": [ [ "imaging/electrophoresis-gel-bands-image-analysis", "Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools", "Imaging", "/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html" ], [ "imaging/iscc-suite", "Content Tracking and Verification in Galaxy Workflows with ISCC-SUM", "Imaging", "/topics/imaging/tutorials/iscc-suite/tutorial.html" ], [ "imaging/process-image-bioimageio", "Using BioImage.IO models for image analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/process-image-bioimageio/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "imgteam/image_info/ip_imageinfo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/8.0.0+galaxy0", "8.0.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/5.7.1+galaxy1", "5.7.1+galaxy1" ] ], "tutorials": [ [ "imaging/electrophoresis-gel-bands-image-analysis", "Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools", "Imaging", "/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html" ], [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "imgteam/2d_simple_filter/ip_filter_standard": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.16.3+galaxy1", "1.16.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1", "1.12.0+galaxy1" ] ], "tutorials": [ [ "imaging/hela-screen-analysis", "Analyse HeLa fluorescence siRNA screen", "Imaging", "/topics/imaging/tutorials/hela-screen-analysis/tutorial.html" ], [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/parameter-tuning", "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy", "Imaging", "/topics/imaging/tutorials/parameter-tuning/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0", "1.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.11.5+galaxy0", "1.11.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy2", "1.10.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0", "1.10.2+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/scanpy_normalize/scanpy_normalize": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3", "1.9.6+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0", "1.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.11.5+galaxy0", "1.11.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy0", "1.10.2+galaxy0" ] ], "tutorials": [ [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "devteam/ncbi_blast_plus/ncbi_blastp_wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.16.0+galaxy0", "2.16.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.14.1+galaxy2", "2.14.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2", "2.10.1+galaxy2" ] ], "tutorials": [ [ "data-science/online-resources-gene", "Learning about one gene across biological resources and formats", "Foundations of Data Science", "/topics/data-science/tutorials/online-resources-gene/tutorial.html" ], [ "genome-annotation/functional", "Functional annotation of protein sequences", "Genome Annotation", "/topics/genome-annotation/tutorials/functional/tutorial.html" ], [ "proteomics/neoantigen-peptide-verification", "Neoantigen 3: PepQuery2 Verification", "Proteomics", "/topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html" ], [ "proteomics/proteogenomics-novel-peptide-analysis", "Proteogenomics 3: Novel peptide analysis", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html" ], [ "sequence-analysis/ncbi-blast-against-the-madland", "NCBI BLAST+ against the MAdLand", "Sequence analysis", "/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html" ] ] }, "interactive_tool_jupyter_notebook": { "tool_id": [ [ "interactive_tool_jupyter_notebook", "interactive_tool_jupyter_notebook" ] ], "tutorials": [ [ "climate/fates-jupyterlab", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab", "Earth Data science", "/topics/climate/tutorials/fates-jupyterlab/tutorial.html" ], [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "galaxy-interface/galaxy-intro-jupyter", "Use Jupyter notebooks in Galaxy", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html" ], [ "galaxy-interface/jupyterlab", "JupyterLab in Galaxy", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/jupyterlab/tutorial.html" ], [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "iuc/volcanoplot/volcanoplot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/3.3.3+galaxy0", "3.3.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7", "0.0.7" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6", "0.0.6" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5", "0.0.5" ] ], "tutorials": [ [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ], [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-volcanoplot", "Visualization of RNA-Seq results with Volcano Plot", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-volcanoplot-r", "Visualization of RNA-Seq results with Volcano Plot in R", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html" ] ] }, "iuc/stringtie/stringtie": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy1", "2.2.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "2.2.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6", "1.3.6" ] ], "tutorials": [ [ "genome-annotation/lncrna", "Long non-coding RNAs (lncRNAs) annotation with FEELnc", "Genome Annotation", "/topics/genome-annotation/tutorials/lncrna/tutorial.html" ], [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/annotatemyids/annotatemyids": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1", "3.5.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1", "3.16.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1", "3.14.0+galaxy1" ] ], "tutorials": [ [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/rna-seq-counts-to-genes", "2: RNA-seq counts to genes", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html" ] ] }, "bgruening/unique/bg_uniq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3", "0.3" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "genome-annotation/bacterial-comparative-genomics-dataset-construction", "Dataset construction for bacterial comparative genomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ] ] }, "devteam/ncbi_blast_plus/ncbi_blastn_wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.16.0+galaxy0", "2.16.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2", "2.14.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1", "2.14.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2", "2.10.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0", "2.10.1+galaxy0" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ], [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "ecology/eDNA-taxonomic-analysis", "Taxonomic Analysis of eDNA", "Ecology", "/topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "iuc/bedtools/bedtools_intersectbed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0", "2.31.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0", "2.30.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0", "2.29.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2", "2.27.0.2" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "introduction/galaxy-intro-101", "Galaxy Basics for genomics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101/tutorial.html" ] ] }, "iuc/bandage/bandage_info": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2", "2022.09+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2", "0.8.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1", "0.8.1+galaxy1" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "assembly/mrsa-illumina", "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data", "Assembly", "/topics/assembly/tutorials/mrsa-illumina/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "bgruening/model_prediction/model_prediction": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3", "1.0.8.3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.2", "1.0.8.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.11.0", "1.0.11.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0", "1.0.10.0" ] ], "tutorials": [ [ "statistics/CNN", "Deep Learning (Part 3) - Convolutional neural networks (CNN)", "Statistics and machine learning", "/topics/statistics/tutorials/CNN/tutorial.html" ], [ "statistics/FNN", "Deep Learning (Part 1) - Feedforward neural networks (FNN)", "Statistics and machine learning", "/topics/statistics/tutorials/FNN/tutorial.html" ], [ "statistics/RNN", "Deep Learning (Part 2) - Recurrent neural networks (RNN)", "Statistics and machine learning", "/topics/statistics/tutorials/RNN/tutorial.html" ], [ "statistics/fruit_360", "Image classification in Galaxy with fruit 360 dataset", "Statistics and machine learning", "/topics/statistics/tutorials/fruit_360/tutorial.html" ], [ "statistics/intro_deep_learning", "Introduction to deep learning", "Statistics and machine learning", "/topics/statistics/tutorials/intro_deep_learning/tutorial.html" ] ] }, "bgruening/keras_train_and_eval/keras_train_and_eval": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3", "1.0.8.3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.2", "1.0.8.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.11.0", "1.0.11.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0", "1.0.10.0" ] ], "tutorials": [ [ "statistics/CNN", "Deep Learning (Part 3) - Convolutional neural networks (CNN)", "Statistics and machine learning", "/topics/statistics/tutorials/CNN/tutorial.html" ], [ "statistics/FNN", "Deep Learning (Part 1) - Feedforward neural networks (FNN)", "Statistics and machine learning", "/topics/statistics/tutorials/FNN/tutorial.html" ], [ "statistics/RNN", "Deep Learning (Part 2) - Recurrent neural networks (RNN)", "Statistics and machine learning", "/topics/statistics/tutorials/RNN/tutorial.html" ], [ "statistics/fruit_360", "Image classification in Galaxy with fruit 360 dataset", "Statistics and machine learning", "/topics/statistics/tutorials/fruit_360/tutorial.html" ], [ "statistics/intro_deep_learning", "Introduction to deep learning", "Statistics and machine learning", "/topics/statistics/tutorials/intro_deep_learning/tutorial.html" ] ] }, "bgruening/keras_model_config/keras_model_config": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0", "1.0.10.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0", "0.5.0" ] ], "tutorials": [ [ "statistics/CNN", "Deep Learning (Part 3) - Convolutional neural networks (CNN)", "Statistics and machine learning", "/topics/statistics/tutorials/CNN/tutorial.html" ], [ "statistics/FNN", "Deep Learning (Part 1) - Feedforward neural networks (FNN)", "Statistics and machine learning", "/topics/statistics/tutorials/FNN/tutorial.html" ], [ "statistics/RNN", "Deep Learning (Part 2) - Recurrent neural networks (RNN)", "Statistics and machine learning", "/topics/statistics/tutorials/RNN/tutorial.html" ], [ "statistics/fruit_360", "Image classification in Galaxy with fruit 360 dataset", "Statistics and machine learning", "/topics/statistics/tutorials/fruit_360/tutorial.html" ], [ "statistics/intro_deep_learning", "Introduction to deep learning", "Statistics and machine learning", "/topics/statistics/tutorials/intro_deep_learning/tutorial.html" ] ] }, "bgruening/keras_model_builder/keras_model_builder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0", "1.0.10.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0", "0.5.0" ] ], "tutorials": [ [ "statistics/CNN", "Deep Learning (Part 3) - Convolutional neural networks (CNN)", "Statistics and machine learning", "/topics/statistics/tutorials/CNN/tutorial.html" ], [ "statistics/FNN", "Deep Learning (Part 1) - Feedforward neural networks (FNN)", "Statistics and machine learning", "/topics/statistics/tutorials/FNN/tutorial.html" ], [ "statistics/RNN", "Deep Learning (Part 2) - Recurrent neural networks (RNN)", "Statistics and machine learning", "/topics/statistics/tutorials/RNN/tutorial.html" ], [ "statistics/fruit_360", "Image classification in Galaxy with fruit 360 dataset", "Statistics and machine learning", "/topics/statistics/tutorials/fruit_360/tutorial.html" ], [ "statistics/intro_deep_learning", "Introduction to deep learning", "Statistics and machine learning", "/topics/statistics/tutorials/intro_deep_learning/tutorial.html" ] ] }, "iuc/seqtk/seqtk_subseq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0", "1.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1", "1.3.1" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ] ] }, "random_lines1": { "tool_id": [ [ "random_lines1", "random_lines1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ], [ "visualisation/circos", "Visualisation with Circos", "Visualisation", "/topics/visualisation/tutorials/circos/tutorial.html" ] ] }, "iuc/compose_text_param/compose_text_param": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "0.1.1" ] ], "tutorials": [ [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "devteam/fasta_compute_length/fasta_compute_length": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", "1.0.4" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3", "1.0.3" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1", "1.0.1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "sequence-analysis/viral_primer_design", "Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes", "Sequence analysis", "/topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html" ], [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "devteam/freebayes/freebayes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.9+galaxy0", "1.3.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0", "1.3.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.10+galaxy1", "1.3.10+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1", "1.3.1" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "variant-analysis/dip", "Calling variants in diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/dip/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ] ] }, "bgruening/get_pdb/get_pdb": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0", "0.1.0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/md-simulation-gromacs", "Running molecular dynamics simulations using GROMACS", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html" ], [ "computational-chemistry/med-chem-data", "Data management in Medicinal Chemistry", "Computational chemistry", "/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html" ], [ "fair/med-chem-data", "Data management in Medicinal Chemistry", "FAIR Data, Workflows, and Research", "/topics/fair/tutorials/med-chem-data/tutorial.html" ] ] }, "bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.4+galaxy0", "3.5.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.5.1.0.1", "3.5.1.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1", "3.3.2.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ] ] }, "bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.4+galaxy0", "3.5.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0", "3.5.1.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0", "3.3.2.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "bgruening/deeptools_bam_coverage/deeptools_bam_coverage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0", "3.5.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0", "3.5.1.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0", "3.3.2.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0", "3.3.0.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "iuc/featurecounts/featurecounts": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.1.1+galaxy0", "2.1.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy1", "2.0.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2", "2.0.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1", "2.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4+galaxy1", "1.6.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3", "1.6.3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2", "1.6.2" ] ], "tutorials": [ [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ] ] }, "__FILTER_FROM_FILE__": { "tool_id": [ [ "__FILTER_FROM_FILE__", "__FILTER_FROM_FILE__" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ], [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "csv_to_tabular": { "tool_id": [ [ "csv_to_tabular", "csv_to_tabular" ] ], "tutorials": [ [ "galaxy-interface/workflow-reports", "Workflow Reports", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-reports/tutorial.html" ], [ "introduction/galaxy-intro-101-everyone", "Galaxy Basics for everyone", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html" ], [ "introduction/galaxy-reproduce", "How to reproduce published Galaxy analyses", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-reproduce/tutorial.html" ], [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "statistics/clustering_machinelearning", "Clustering in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/clustering_machinelearning/tutorial.html" ] ] }, "__UNZIP_COLLECTION__": { "tool_id": [ [ "__UNZIP_COLLECTION__", "__UNZIP_COLLECTION__" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ] ] }, "interactive_tool_odv": { "tool_id": [ [ "interactive_tool_odv", "interactive_tool_odv" ] ], "tutorials": [ [ "climate/argo_pangeo", "Analyse Argo data", "Earth Data science", "/topics/climate/tutorials/argo_pangeo/tutorial.html" ], [ "climate/ocean-data-view", "Ocean Data View (ODV)", "Earth Data science", "/topics/climate/tutorials/ocean-data-view/tutorial.html" ], [ "climate/ocean-variables", "Ocean's variables study", "Earth Data science", "/topics/climate/tutorials/ocean-variables/tutorial.html" ], [ "climate/ocean_qcv_analysis", "Nitrate DMQC for autonomous platforms such as Argo floats", "Earth Data science", "/topics/climate/tutorials/ocean_qcv_analysis/tutorial.html" ] ] }, "ecology/xarray_metadata_info/xarray_metadata_info": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+galaxy0", "2022.3.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1", "0.15.1" ] ], "tutorials": [ [ "climate/argo_pangeo", "Analyse Argo data", "Earth Data science", "/topics/climate/tutorials/argo_pangeo/tutorial.html" ], [ "climate/fates", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", "Earth Data science", "/topics/climate/tutorials/fates/tutorial.html" ], [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "ecology/x-array-map-plot", "Visualization of Climate Data using NetCDF xarray Map Plotting", "Ecology", "/topics/ecology/tutorials/x-array-map-plot/tutorial.html" ] ] }, "devteam/bwa/bwa": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.19", "0.7.19" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5", "0.7.17.5" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4", "0.7.17.4" ] ], "tutorials": [ [ "admin/reference-genomes", "Reference Data with Data Managers", "Galaxy Server administration", "/topics/admin/tutorials/reference-genomes/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ] ] }, "wc_gnu": { "tool_id": [ [ "wc_gnu", "wc_gnu" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "imgteam/bfconvert/ip_convertimage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3", "6.7.0+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0", "6.7.0+galaxy0" ] ], "tutorials": [ [ "imaging/biapy", "Execute a BiaPy workflow in Galaxy", "Imaging", "/topics/imaging/tutorials/biapy/tutorial.html" ], [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "iuc/column_remove_by_header/column_remove_by_header": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0", "1.0" ] ], "tutorials": [ [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ], [ "introduction/galaxy-intro-rdm", "Introduction to Galaxy as an RDM platform", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ], [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ] ] }, "ebi-gxa/retrieve_scxa/retrieve_scxa": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2", "v0.0.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1", "v0.0.1+galaxy1" ] ], "tutorials": [ [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "bgruening/music_construct_eset/music_construct_eset": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4", "0.1.1+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy3", "0.1.1+galaxy3" ] ], "tutorials": [ [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music", "Bulk RNA Deconvolution with MuSiC", "Single Cell", "/topics/single-cell/tutorials/bulk-music/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ] ] }, "ebi-gxa/scanpy_compute_graph/scanpy_compute_graph": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.9.3+galaxy0", "1.9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1", "1.8.1+galaxy1" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ], [ "single-cell/scanpy_parameter_iterator", "Scanpy Parameter Iterator", "Single Cell", "/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "iuc/newick_utils/newick_display": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1", "1.6+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6", "1.6" ] ], "tutorials": [ [ "evolution/abc_intro_phylo", "Phylogenetics - Back to basics", "Evolution", "/topics/evolution/tutorials/abc_intro_phylo/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/iqtree/iqtree": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.4.0+galaxy2", "2.4.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.3.6+galaxy0", "2.3.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2", "2.1.2+galaxy2" ] ], "tutorials": [ [ "evolution/abc_intro_phylo", "Phylogenetics - Back to basics", "Evolution", "/topics/evolution/tutorials/abc_intro_phylo/tutorial.html" ], [ "genome-annotation/pangenome-annotation-with-roary", "Pangenome analysis with Roary", "Genome Annotation", "/topics/genome-annotation/tutorials/pangenome-annotation-with-roary/tutorial.html" ], [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ] ] }, "galaxyp/uniprotxml_downloader/uniprotxml_downloader": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0", "2.4.0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.3.0", "2.3.0" ] ], "tutorials": [ [ "microbiome/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html" ], [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ] ] }, "galaxyp/unipept/unipept": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/6.2.4+galaxy1", "6.2.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.1", "4.5.1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0", "4.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0", "4.3.0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0", "4.0.0" ] ], "tutorials": [ [ "microbiome/clinical-mp-5-data-interpretation", "Clinical Metaproteomics 5: Data Interpretation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-5-data-interpretation/tutorial.html" ], [ "proteomics/clinical-mp-5-data-interpretation", "Clinical Metaproteomics 5: Data Interpretation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html" ], [ "proteomics/metaproteomics", "Metaproteomics tutorial", "Proteomics", "/topics/proteomics/tutorials/metaproteomics/tutorial.html" ], [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ] ] }, "wig_to_bigWig": { "tool_id": [ [ "wig_to_bigWig", "wig_to_bigWig" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "iuc/gffcompare/gffcompare": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.6+galaxy0", "0.12.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.10+galaxy0", "0.12.10+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2", "0.11.2" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ], [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/meryl/meryl": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "1.3+galaxy6" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4", "1.3+galaxy4" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-quality-control", "Genome Assembly Quality Control", "Assembly", "/topics/assembly/tutorials/assembly-quality-control/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "bgruening/diamond/bg_diamond": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0", "2.0.15+galaxy0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "genome-annotation/functional", "Functional annotation of protein sequences", "Genome Annotation", "/topics/genome-annotation/tutorials/functional/tutorial.html" ], [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "sequence-analysis/ncbi-blast-against-the-madland", "NCBI BLAST+ against the MAdLand", "Sequence analysis", "/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html" ] ] }, "iuc/porechop/porechop": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0", "0.2.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4", "0.2.4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3", "0.2.3" ] ], "tutorials": [ [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "microbiome/beer-data-analysis", "Identification of the micro-organisms in a beer using Nanopore sequencing", "Microbiome", "/topics/microbiome/tutorials/beer-data-analysis/tutorial.html" ], [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/bwa_mem2/bwa_mem2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4", "2.2.1+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "2.2.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0", "2.2.1+galaxy0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ] ] }, "devteam/merge_cols/mergeCols1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2", "1.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1", "1.0.1" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ], [ "transcriptomics/rna-seq-counts-to-genes", "2: RNA-seq counts to genes", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html" ] ] }, "iuc/unicycler/unicycler": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", "0.5.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0", "0.4.8.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0", "0.4.7.0" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/hybrid_denovo_assembly", "Hybrid genome assembly - Nanopore and Illumina", "Assembly", "/topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html" ], [ "assembly/unicycler-assembly", "Unicycler Assembly", "Assembly", "/topics/assembly/tutorials/unicycler-assembly/tutorial.html" ], [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "bgruening/ml_visualization_ex/ml_visualization_ex": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3", "1.0.8.3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2", "1.0.8.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.11.0", "1.0.11.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.10.0", "1.0.10.0" ] ], "tutorials": [ [ "statistics/CNN", "Deep Learning (Part 3) - Convolutional neural networks (CNN)", "Statistics and machine learning", "/topics/statistics/tutorials/CNN/tutorial.html" ], [ "statistics/RNN", "Deep Learning (Part 2) - Recurrent neural networks (RNN)", "Statistics and machine learning", "/topics/statistics/tutorials/RNN/tutorial.html" ], [ "statistics/fruit_360", "Image classification in Galaxy with fruit 360 dataset", "Statistics and machine learning", "/topics/statistics/tutorials/fruit_360/tutorial.html" ], [ "statistics/intro_deep_learning", "Introduction to deep learning", "Statistics and machine learning", "/topics/statistics/tutorials/intro_deep_learning/tutorial.html" ] ] }, "lecorguille/xcms_xcmsset/abims_xcms_xcmsSet": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.4.4.1", "3.4.4.1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy1", "3.12.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ], [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "lecorguille/xcms_merge/xcms_merge": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.4.4.0", "3.4.4.0" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy1", "3.12.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ], [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "lecorguille/xcms_group/abims_xcms_group": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.4.4.0", "3.4.4.0" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy1", "3.12.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ], [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.4.4.0", "3.4.4.0" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy1", "3.12.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ], [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "lecorguille/msnbase_readmsdata/msnbase_readmsdata": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.8.2.1", "2.8.2.1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy2", "2.16.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0", "2.16.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ], [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "iuc/snpsift/snpSift_extractFields": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0", "4.3+t.galaxy0" ] ], "tutorials": [ [ "galaxy-interface/collections", "Using dataset collections", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/collections/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "__ZIP_COLLECTION__": { "tool_id": [ [ "__ZIP_COLLECTION__", "__ZIP_COLLECTION__" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "microbiome/host-removal", "Remove contamination and host reads", "Microbiome", "/topics/microbiome/tutorials/host-removal/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "iuc/gemini_load/gemini_load": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2", "0.20.1+galaxy2" ] ], "tutorials": [ [ "variant-analysis/dip", "Calling variants in diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/dip/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/bcftools_consensus/bcftools_consensus": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2", "1.9+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy1", "1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4", "1.15.1+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3", "1.15.1+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10", "1.10" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/circos/circos": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9", "0.69.8+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7", "0.69.8+galaxy7" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12", "0.69.8+galaxy12" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "visualisation/circos", "Visualisation with Circos", "Visualisation", "/topics/visualisation/tutorials/circos/tutorial.html" ], [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "bgruening/deeptools_plot_correlation/deeptools_plot_correlation": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0", "3.5.1.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0", "3.3.2.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.1.0.0", "3.5.1.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0", "3.3.2.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "devteam/freebayes/bamleftalign": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.9", "1.3.9" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.8", "1.3.8" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6", "1.3.6" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1", "1.3.1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0", "1.1.0.46-0" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "nilesh/rseqc/rseqc_read_distribution": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0", "5.0.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2", "5.0.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1", "2.6.4.1" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ] ] }, "nilesh/rseqc/rseqc_geneBody_coverage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0", "5.0.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2", "5.0.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3", "2.6.4.3" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ] ] }, "iuc/pygenometracks/pygenomeTracks": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.9+galaxy0", "3.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2", "3.8+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy1", "3.8+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6", "3.6" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "iuc/goseq/goseq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0", "1.50.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0", "1.44.0+galaxy0" ] ], "tutorials": [ [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ] ] }, "iuc/ggplot2_heatmap2/ggplot2_heatmap2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1", "3.2.0+galaxy1" ] ], "tutorials": [ [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ] ] }, "bgruening/sklearn_ensemble/sklearn_ensemble": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1", "1.0.8.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.2", "1.0.11.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "1.0.11.0" ] ], "tutorials": [ [ "statistics/age-prediction-with-ml", "Age prediction using machine learning", "Statistics and machine learning", "/topics/statistics/tutorials/age-prediction-with-ml/tutorial.html" ], [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ], [ "statistics/classification_regression", "Machine learning: classification and regression", "Statistics and machine learning", "/topics/statistics/tutorials/classification_regression/tutorial.html" ], [ "statistics/regression_machinelearning", "Regression in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/regression_machinelearning/tutorial.html" ] ] }, "bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1", "0.1" ] ], "tutorials": [ [ "statistics/FNN", "Deep Learning (Part 1) - Feedforward neural networks (FNN)", "Statistics and machine learning", "/topics/statistics/tutorials/FNN/tutorial.html" ], [ "statistics/age-prediction-with-ml", "Age prediction using machine learning", "Statistics and machine learning", "/topics/statistics/tutorials/age-prediction-with-ml/tutorial.html" ], [ "statistics/classification_regression", "Machine learning: classification and regression", "Statistics and machine learning", "/topics/statistics/tutorials/classification_regression/tutorial.html" ], [ "statistics/regression_machinelearning", "Regression in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/regression_machinelearning/tutorial.html" ] ] }, "crs4/prokka/prokka": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.6+galaxy2", "1.14.6+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0", "1.14.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5", "1.14.5" ] ], "tutorials": [ [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/unicycler-assembly", "Unicycler Assembly", "Assembly", "/topics/assembly/tutorials/unicycler-assembly/tutorial.html" ], [ "genome-annotation/annotation-with-prokka", "Genome annotation with Prokka", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html" ], [ "genome-annotation/pangenome-annotation-with-roary", "Pangenome analysis with Roary", "Genome Annotation", "/topics/genome-annotation/tutorials/pangenome-annotation-with-roary/tutorial.html" ] ] }, "devteam/histogram/histogram_rpy": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4", "1.0.4" ] ], "tutorials": [ [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "proteomics/DIA_Analysis_MSstats", "Statistical analysis of DIA data", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "devteam/fastq_groomer/fastq_groomer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5+galaxy2", "1.1.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5", "1.1.5" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "ecology/spocc_occ/spocc_occ": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ/0.9.0", "0.9.0" ] ], "tutorials": [ [ "climate/earth_system", "Getting your hands-on earth data", "Earth Data science", "/topics/climate/tutorials/earth_system/tutorial.html" ], [ "ecology/gbif_cleaning", "Cleaning GBIF data for the use in Ecology", "Ecology", "/topics/ecology/tutorials/gbif_cleaning/tutorial.html" ], [ "ecology/species-distribution-modeling", "Species distribution modeling", "Ecology", "/topics/ecology/tutorials/species-distribution-modeling/tutorial.html" ] ] }, "devteam/fastqtofasta/fastq_to_fasta_python": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5+galaxy2", "1.1.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5", "1.1.5" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "galaxy-interface/ncbi-sarf", "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "__FILTER_EMPTY_DATASETS__": { "tool_id": [ [ "__FILTER_EMPTY_DATASETS__", "__FILTER_EMPTY_DATASETS__" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/drep_dereplicate/drep_dereplicate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.6.2+galaxy1", "3.6.2+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.5.0+galaxy1", "3.5.0+galaxy1" ] ], "tutorials": [ [ "genome-annotation/bacterial-genome-quality-control", "Bacterial genome quality control", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/metaphlan/metaphlan": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.1.1+galaxy4", "4.1.1+galaxy4" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ], [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ] ] }, "iuc/krakentools_kreport2krona/krakentools_kreport2krona": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy2", "1.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1", "1.2+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0", "1.2+galaxy0" ] ], "tutorials": [ [ "microbiome/beer-data-analysis", "Identification of the micro-organisms in a beer using Nanopore sequencing", "Microbiome", "/topics/microbiome/tutorials/beer-data-analysis/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ] ] }, "iuc/bracken/est_abundance": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0", "3.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0", "2.9+galaxy0" ] ], "tutorials": [ [ "ecology/bacterial-isolate-species-contamination-checking", "Checking expected species and contamination in bacterial isolate", "Ecology", "/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html" ], [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ], [ "sequence-analysis/quality-contamination-control", "Quality and contamination control in bacterial isolate using Illumina MiSeq Data", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html" ] ] }, "ecology/xarray_coords_info/xarray_coords_info": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0", "2022.3.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0", "0.20.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.18.2+galaxy0", "0.18.2+galaxy0" ] ], "tutorials": [ [ "climate/argo_pangeo", "Analyse Argo data", "Earth Data science", "/topics/climate/tutorials/argo_pangeo/tutorial.html" ], [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "ecology/x-array-map-plot", "Visualization of Climate Data using NetCDF xarray Map Plotting", "Ecology", "/topics/ecology/tutorials/x-array-map-plot/tutorial.html" ] ] }, "iuc/ggplot2_histogram/ggplot2_histogram": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/3.5.1+galaxy1", "3.5.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/3.4.0+galaxy0", "3.4.0+galaxy0" ] ], "tutorials": [ [ "introduction/galaxy-intro-rdm", "Introduction to Galaxy as an RDM platform", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html" ], [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "variant-analysis/countess-mave-chek2", "Calculating CHEK2 variant effect scores from MAVE data with CountESS", "Variant Analysis", "/topics/variant-analysis/tutorials/countess-mave-chek2/tutorial.html" ] ] }, "tabular_to_csv": { "tool_id": [ [ "tabular_to_csv", "tabular_to_csv" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "ecology/species-distribution-modeling", "Species distribution modeling", "Ecology", "/topics/ecology/tutorials/species-distribution-modeling/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.45+galaxy0", "1.3.45+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.40+galaxy0", "1.3.40+galaxy0" ] ], "tutorials": [ [ "galaxy-interface/workflow-posters", "Creating high resolution images of Galaxy Workflows", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-posters/tutorial.html" ], [ "imaging/electrophoresis-gel-bands-image-analysis", "Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools", "Imaging", "/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html" ], [ "imaging/yolo-segmentation-training", "Training Custom YOLO Models for Segmentation of Bioimages", "Imaging", "/topics/imaging/tutorials/yolo-segmentation-training/tutorial.html" ] ] }, "iuc/idr_download_by_ids/idr_download_by_ids": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.45", "0.45" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41", "0.41" ] ], "tutorials": [ [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "imgteam/libcarna_render/libcarna_render": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/libcarna_render/libcarna_render/0.2.0+galaxy2", "0.2.0+galaxy2" ] ], "tutorials": [ [ "imaging/biapy", "Execute a BiaPy workflow in Galaxy", "Imaging", "/topics/imaging/tutorials/biapy/tutorial.html" ], [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "bgruening/add_line_to_file/add_line_to_file": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0", "0.1.0" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ] ] }, "iuc/sceasy_convert/sceasy_convert": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2", "0.0.7+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy1", "0.0.7+galaxy1" ] ], "tutorials": [ [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "ebi-gxa/seurat_read10x/seurat_read10x": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0", "4.0.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0", "3.2.3+galaxy0" ] ], "tutorials": [ [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "iuc/scanpy_remove_confounders/scanpy_remove_confounders": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0", "1.7.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.11.5+galaxy0", "1.11.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy0", "1.10.2+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "ebi-gxa/scanpy_plot_embed/scanpy_plot_embed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scanpy_parameter_iterator", "Scanpy Parameter Iterator", "Single Cell", "/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "ebi-gxa/scanpy_find_cluster/scanpy_find_cluster": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scanpy_parameter_iterator", "Scanpy Parameter Iterator", "Single Cell", "/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "iuc/anndata_import/anndata_import": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0", "0.7.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0", "0.10.9+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ], [ "single-cell/scrna-plant", "Analysis of plant scRNA-Seq Data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-plant/tutorial.html" ], [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ] ] }, "ebi-gxa/scanpy_filter_cells/scanpy_filter_cells": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.9.3+galaxy0", "1.9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy93", "1.8.1+galaxy93" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "single-cell/scrna-ncbi-anndata", "Converting NCBI Data to the AnnData Format", "Single Cell", "/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html" ] ] }, "bgruening/wordcloud/wordcloud": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/wordcloud/wordcloud/1.9.6+galaxy0", "1.9.6+galaxy0" ] ], "tutorials": [ [ "digital-humanities/introduction_to_dh", "Introduction to Digital Humanities in Galaxy", "Digital Humanities", "/topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ] ] }, "iuc/fasttree/fasttree": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1", "2.1.10+galaxy1" ] ], "tutorials": [ [ "evolution/abc_intro_phylo", "Phylogenetics - Back to basics", "Evolution", "/topics/evolution/tutorials/abc_intro_phylo/tutorial.html" ], [ "evolution/bacterial-comparative-genomics", "Phylogenetic analysis for bacterial comparative genomics", "Evolution", "/topics/evolution/tutorials/bacterial-comparative-genomics/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "galaxyp/peptideshaker/ident_params": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1", "4.0.41+galaxy1" ] ], "tutorials": [ [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/proteogenomics-dbsearch", "Proteogenomics 2: Database Search", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" ] ] }, "proteore/proteore_filter_keywords_values/MQoutputfilter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2021.04.19.1", "2021.04.19.1" ], [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11", "2019.03.11" ], [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.05", "2019.03.05" ] ], "tutorials": [ [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ], [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ], [ "proteomics/proteome_annotation", "Annotating a protein list identified by LC-MS/MS experiments", "Proteomics", "/topics/proteomics/tutorials/proteome_annotation/tutorial.html" ] ] }, "galaxyp/pepquery2/pepquery2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy2", "2.0.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy0", "2.0.2+galaxy0" ] ], "tutorials": [ [ "microbiome/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/clinical-mp-3-verification", "Clinical Metaproteomics 3: Verification", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html" ], [ "proteomics/neoantigen-peptide-verification", "Neoantigen 3: PepQuery2 Verification", "Proteomics", "/topics/proteomics/tutorials/neoantigen-peptide-verification/tutorial.html" ] ] }, "galaxyp/msstatstmt/msstatstmt": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy1", "2.0.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0", "2.0.0+galaxy0" ] ], "tutorials": [ [ "microbiome/clinical-mp-5-data-interpretation", "Clinical Metaproteomics 5: Data Interpretation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-5-data-interpretation/tutorial.html" ], [ "proteomics/clinical-mp-5-data-interpretation", "Clinical Metaproteomics 5: Data Interpretation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html" ], [ "proteomics/maxquant-msstats-tmt", "MaxQuant and MSstats for the analysis of TMT data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html" ] ] }, "devteam/clustalw/clustalw": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1", "2.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1", "2.1" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "genome-annotation/hpc-for-lsgc", "From small to large-scale genome comparison", "Genome Annotation", "/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "bgruening/interproscan/interproscan": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3", "5.59-91.0+galaxy3" ] ], "tutorials": [ [ "ecology/marine_omics_bgc", "Marine Omics identifying biosynthetic gene clusters", "Ecology", "/topics/ecology/tutorials/marine_omics_bgc/tutorial.html" ], [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ], [ "genome-annotation/functional", "Functional annotation of protein sequences", "Genome Annotation", "/topics/genome-annotation/tutorials/functional/tutorial.html" ] ] }, "iuc/bakta/bakta": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy1", "1.9.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0", "1.9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0", "1.8.2+galaxy0" ] ], "tutorials": [ [ "genome-annotation/amr-gene-detection", "Identification of AMR genes in an assembled bacterial genome", "Genome Annotation", "/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html" ], [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ], [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ] ] }, "iuc/omark/omark": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.1+galaxy0", "0.3.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/omark/omark/0.3.0+galaxy2", "0.3.0+galaxy2" ] ], "tutorials": [ [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ], [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ], [ "genome-annotation/helixer", "Genome annotation with Helixer", "Genome Annotation", "/topics/genome-annotation/tutorials/helixer/tutorial.html" ] ] }, "iuc/jcvi_gff_stats/jcvi_gff_stats": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/view/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4", "0.8.4" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4", "0.8.4" ] ], "tutorials": [ [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ], [ "genome-annotation/annotation-with-maker-short", "Genome annotation with Maker (short)", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html" ], [ "genome-annotation/helixer", "Genome annotation with Helixer", "Genome Annotation", "/topics/genome-annotation/tutorials/helixer/tutorial.html" ] ] }, "iuc/umi_tools_extract/umi_tools_extract": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.6+galaxy0", "1.1.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2", "1.1.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1", "0.5.5.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2", "0.5.3.2" ] ], "tutorials": [ [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ], [ "single-cell/scrna-umis", "Understanding Barcodes", "Single Cell", "/topics/single-cell/tutorials/scrna-umis/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "__SORTLIST__": { "tool_id": [ [ "__SORTLIST__", "__SORTLIST__" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "galaxyp/filter_by_fasta_ids/filter_by_fasta_ids": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3", "2.3" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ], [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ], [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ] ] }, "addValue": { "tool_id": [ [ "addValue", "addValue" ] ], "tutorials": [ [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ], [ "proteomics/database-handling", "Protein FASTA Database Handling", "Proteomics", "/topics/proteomics/tutorials/database-handling/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "barchart_gnuplot": { "tool_id": [ [ "barchart_gnuplot", "barchart_gnuplot" ] ], "tutorials": [ [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/gfa_to_fa/gfa_to_fa": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2", "0.1.2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.1", "0.1.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0", "0.1.0" ] ], "tutorials": [ [ "assembly/hifi-assembly", "Genome assembly using PacBio data", "Assembly", "/topics/assembly/tutorials/hifi-assembly/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "iuc/bedtools/bedtools_bamtobed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0", "2.31.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2", "2.30.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0", "2.30.0" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ], [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ] ] }, "iuc/merqury/merqury": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3", "1.3+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2", "1.3+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1", "1.3+galaxy1" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-quality-control", "Genome Assembly Quality Control", "Assembly", "/topics/assembly/tutorials/assembly-quality-control/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "iuc/genomescope/genomescope": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", "2.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1", "2.0+galaxy1" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "bgruening/gfastats/gfastats": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "1.3.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0", "1.2.0+galaxy0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "devteam/add_value/addValue": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1", "1.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0", "1.0.0" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/samtools_fastx/samtools_fastx": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1", "1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2", "1.15.1+galaxy2" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "sequence-analysis/human-reads-removal", "Removal of human reads from SARS-CoV-2 sequencing data", "Sequence analysis", "/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html" ] ] }, "bgruening/flexynesis_plot/flexynesis_plot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_plot/flexynesis_plot/1.1.10+galaxy0", "1.1.10+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_plot/flexynesis_plot/0.2.20+galaxy3", "0.2.20+galaxy3" ] ], "tutorials": [ [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "statistics/flexynesis_survival", "Identifing Survival Markers of Brain tumor with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_survival/tutorial.html" ], [ "statistics/flexynesis_unsupervised", "Unsupervised Analysis of Bone Marrow Cells with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_unsupervised/tutorial.html" ] ] }, "bgruening/flexynesis/flexynesis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/1.1.10+galaxy0", "1.1.10+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/0.2.20+galaxy3", "0.2.20+galaxy3" ] ], "tutorials": [ [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ], [ "statistics/flexynesis_survival", "Identifing Survival Markers of Brain tumor with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_survival/tutorial.html" ], [ "statistics/flexynesis_unsupervised", "Unsupervised Analysis of Bone Marrow Cells with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_unsupervised/tutorial.html" ] ] }, "bgruening/sklearn_searchcv/sklearn_searchcv": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1", "1.0.8.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.2", "1.0.11.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0", "1.0.11.0" ] ], "tutorials": [ [ "statistics/age-prediction-with-ml", "Age prediction using machine learning", "Statistics and machine learning", "/topics/statistics/tutorials/age-prediction-with-ml/tutorial.html" ], [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ], [ "statistics/regression_machinelearning", "Regression in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/regression_machinelearning/tutorial.html" ] ] }, "bgruening/sklearn_build_pipeline/sklearn_build_pipeline": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1", "1.0.8.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.2", "1.0.11.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0", "1.0.11.0" ] ], "tutorials": [ [ "statistics/age-prediction-with-ml", "Age prediction using machine learning", "Statistics and machine learning", "/topics/statistics/tutorials/age-prediction-with-ml/tutorial.html" ], [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ], [ "statistics/regression_machinelearning", "Regression in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/regression_machinelearning/tutorial.html" ] ] }, "devteam/fastq_to_tabular/fastq_to_tabular": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5", "1.1.5" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1", "1.1.1" ] ], "tutorials": [ [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "lecorguille/xcms_retcor/abims_xcms_retcor": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.4.4.1", "3.4.4.1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy1", "3.12.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.4.4.0", "3.4.4.0" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy3", "3.12.0+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy1", "3.12.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata/3.12.0+galaxy3", "3.12.0+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata/3.12.0+galaxy1", "3.12.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ], [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "galaxyp/cardinal_quality_report/cardinal_quality_report": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1", "2.6.0.1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3", "1.12.1.3" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2", "1.12.1.2" ] ], "tutorials": [ [ "metabolomics/msi-analyte-distribution", "Mass spectrometry imaging: Examining the spatial distribution of analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html" ], [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ], [ "proteomics/mass-spectrometry-imaging-loading-exploring-data", "Mass spectrometry imaging: Loading and exploring MSI data", "Proteomics", "/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html" ] ] }, "iuc/snpeff_sars_cov_2/snpeff_sars_cov_2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19", "4.5covid19" ] ], "tutorials": [ [ "galaxy-interface/ncbi-sarf", "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "iuc/lofreq_call/lofreq_call": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3", "2.1.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1", "2.1.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0", "2.1.5+galaxy0" ] ], "tutorials": [ [ "galaxy-interface/collections", "Using dataset collections", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/collections/tutorial.html" ], [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "iuc/bcftools_norm/bcftools_norm": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1", "1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.22+galaxy0", "1.22+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3", "1.15.1+galaxy3" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/snippy/snippy": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0", "4.6.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2", "3.2" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "variant-analysis/microbial-variants", "Microbial Variant Calling", "Variant Analysis", "/topics/variant-analysis/tutorials/microbial-variants/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/qualimap_bamqc/qualimap_bamqc": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0", "2.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3", "2.2.2d+galaxy3" ] ], "tutorials": [ [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "devteam/samtools_rmdup/samtools_rmdup": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1", "2.0.1" ] ], "tutorials": [ [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "bgruening/text_processing/tp_text_file_with_recurring_lines": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3", "9.5+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2", "9.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0", "1.1.0" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ] ] }, "__RELABEL_FROM_FILE__": { "tool_id": [ [ "__RELABEL_FROM_FILE__", "__RELABEL_FROM_FILE__" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ] ] }, "__BUILD_LIST__": { "tool_id": [ [ "__BUILD_LIST__", "__BUILD_LIST__" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ] ] }, "chemteam/md_converter/md_converter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0", "1.9.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.3.2", "1.9.3.2" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/med-chem-data", "Data management in Medicinal Chemistry", "Computational chemistry", "/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html" ], [ "fair/med-chem-data", "Data management in Medicinal Chemistry", "FAIR Data, Workflows, and Research", "/topics/fair/tutorials/med-chem-data/tutorial.html" ] ] }, "bgruening/qed/ctb_silicos_qed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0", "2021.03.4+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/med-chem-data", "Data management in Medicinal Chemistry", "Computational chemistry", "/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html" ], [ "fair/med-chem-data", "Data management in Medicinal Chemistry", "FAIR Data, Workflows, and Research", "/topics/fair/tutorials/med-chem-data/tutorial.html" ], [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "bgruening/openbabel_svg_depiction/openbabel_svg_depiction": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy1", "3.1.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0", "3.1.1+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "computational-chemistry/med-chem-data", "Data management in Medicinal Chemistry", "Computational chemistry", "/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html" ], [ "fair/med-chem-data", "Data management in Medicinal Chemistry", "FAIR Data, Workflows, and Research", "/topics/fair/tutorials/med-chem-data/tutorial.html" ] ] }, "bgruening/chembl/chembl": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4", "0.10.1+galaxy4" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "computational-chemistry/med-chem-data", "Data management in Medicinal Chemistry", "Computational chemistry", "/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html" ], [ "fair/med-chem-data", "Data management in Medicinal Chemistry", "FAIR Data, Workflows, and Research", "/topics/fair/tutorials/med-chem-data/tutorial.html" ] ] }, "iuc/bedtools/bedtools_sortbed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.31.1+galaxy0", "2.31.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2", "2.30.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0", "2.27.0.0" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ] ] }, "bgruening/deeptools_bam_compare/deeptools_bam_compare": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.1.0.0", "3.5.1.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0", "3.3.2.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ] ] }, "nilesh/rseqc/rseqc_infer_experiment": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0", "5.0.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1", "2.6.4.1" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-reads-to-counts", "1: RNA-Seq reads to counts", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html" ] ] }, "fubar/jbrowse2/jbrowse2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0", "3.7.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.6.5+galaxy1", "3.6.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/2.17.0+galaxy0", "2.17.0+galaxy0" ] ], "tutorials": [ [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "visualisation/jbrowse2", "Genomic Data Visualisation with JBrowse2", "Visualisation", "/topics/visualisation/tutorials/jbrowse2/tutorial.html" ] ] }, "bgruening/sklearn_svm_classifier/sklearn_svm_classifier": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1", "1.0.8.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.11.2", "1.0.11.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.11.0", "1.0.11.0" ] ], "tutorials": [ [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ], [ "statistics/classification_regression", "Machine learning: classification and regression", "Statistics and machine learning", "/topics/statistics/tutorials/classification_regression/tutorial.html" ], [ "statistics/machinelearning", "Basics of machine learning", "Statistics and machine learning", "/topics/statistics/tutorials/machinelearning/tutorial.html" ] ] }, "devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0", "1.2.0.1+galaxy0" ] ], "tutorials": [ [ "assembly/general-introduction", "An Introduction to Genome Assembly", "Assembly", "/topics/assembly/tutorials/general-introduction/tutorial.html" ], [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/mothur_unique_seqs/mothur_unique_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_summary_seqs/mothur_summary_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_screen_seqs/mothur_screen_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1", "1.39.5.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_pre_cluster/mothur_pre_cluster": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_make_shared/mothur_make_shared": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_filter_seqs/mothur_filter_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_count_seqs/mothur_count_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_cluster_split/mothur_cluster_split": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_classify_seqs/mothur_classify_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_classify_otu/mothur_classify_otu": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "galaxyp/msstats/msstats": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/4.0.0+galaxy1", "4.0.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0", "3.20.1.0" ] ], "tutorials": [ [ "proteomics/DIA_Analysis_MSstats", "Statistical analysis of DIA data", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html" ], [ "proteomics/maxquant-label-free", "Label-free data analysis using MaxQuant", "Proteomics", "/topics/proteomics/tutorials/maxquant-label-free/tutorial.html" ], [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ] ] }, "devteam/intersect/gops_intersect_1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0", "1.0.0" ] ], "tutorials": [ [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ], [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ], [ "introduction/galaxy-intro-strands", "Introduction to Genomics and Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html" ] ] }, "iuc/beacon2_cnv/beacon2_cnv": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/beacon2_cnv/beacon2_cnv/2.1.1+galaxy0", "2.1.1+galaxy0" ] ], "tutorials": [ [ "variant-analysis/beacon_cnv_query", "Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)", "Variant Analysis", "/topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.html" ], [ "variant-analysis/beaconise_1000hg", "Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons", "Variant Analysis", "/topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html" ] ] }, "melpetera/intensity_checks/intens_check": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8", "1.2.8" ] ], "tutorials": [ [ "metabolomics/lcms-dataprocessing", "Mass spectrometry: LC-MS data processing", "Metabolomics", "/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "ecology/ab1_fastq_converter/ab1_fastq_converter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0", "1.20.0" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "devteam/fastq_to_fasta/cshl_fastq_to_fasta": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2+galaxy2", "1.0.2+galaxy2" ] ], "tutorials": [ [ "ecology/eDNA-taxonomic-analysis", "Taxonomic Analysis of eDNA", "Ecology", "/topics/ecology/tutorials/eDNA-taxonomic-analysis/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "ecology/sam3_semantic_segmentation/sam3_semantic_segmentation": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/sam3_semantic_segmentation/sam3_semantic_segmentation/1.0.1+galaxy6", "1.0.1+galaxy6" ], [ "toolshed.g2.bx.psu.edu/repos/ecology/sam3_semantic_segmentation/sam3_semantic_segmentation/1.0.1+galaxy4", "1.0.1+galaxy4" ] ], "tutorials": [ [ "ecology/SAM3", "SAM3 – AI-based Semantic Segmentation of marine biodiversity Images and Videos", "Ecology", "/topics/ecology/tutorials/SAM3/tutorial.html" ], [ "imaging/Annotation_AI_Pipeline", "AI pipeline for annotating marine species (Project Moorev - Marine)", "Imaging", "/topics/imaging/tutorials/Annotation_AI_Pipeline/tutorial.html" ] ] }, "ecology/obis_data/obis_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2", "0.0.2" ] ], "tutorials": [ [ "climate/earth_system", "Getting your hands-on earth data", "Earth Data science", "/topics/climate/tutorials/earth_system/tutorial.html" ], [ "ecology/obisindicators", "Obis marine indicators", "Ecology", "/topics/ecology/tutorials/obisindicators/tutorial.html" ] ] }, "iuc/stacks_procrad/stacks_procrad": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0", "1.46.0" ] ], "tutorials": [ [ "ecology/de-novo-rad-seq", "RAD-Seq de-novo data analysis", "Ecology", "/topics/ecology/tutorials/de-novo-rad-seq/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ] ] }, "iuc/stacks_populations/stacks_populations": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0", "1.46.0" ] ], "tutorials": [ [ "ecology/de-novo-rad-seq", "RAD-Seq de-novo data analysis", "Ecology", "/topics/ecology/tutorials/de-novo-rad-seq/tutorial.html" ], [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ] ] }, "iuc/stacks_denovomap/stacks_denovomap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0", "1.46.0" ] ], "tutorials": [ [ "ecology/de-novo-rad-seq", "RAD-Seq de-novo data analysis", "Ecology", "/topics/ecology/tutorials/de-novo-rad-seq/tutorial.html" ], [ "ecology/genetic-map-rad-seq", "RAD-Seq to construct genetic maps", "Ecology", "/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html" ] ] }, "iuc/recentrifuge/recentrifuge": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0", "1.16.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0", "1.12.1+galaxy0" ] ], "tutorials": [ [ "ecology/bacterial-isolate-species-contamination-checking", "Checking expected species and contamination in bacterial isolate", "Ecology", "/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html" ], [ "sequence-analysis/quality-contamination-control", "Quality and contamination control in bacterial isolate using Illumina MiSeq Data", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html" ] ] }, "ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ] ] }, "ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ] ] }, "ecology/ecoregion_eco_map/ecoregion_eco_map": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/ecoregion_eco_map/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ] ] }, "ecology/ecoregion_brt_analysis/ecoregion_brt_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_brt_analysis/ecoregion_brt_analysis/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ], [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ] ] }, "devteam/fastq_filter/fastq_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2", "1.1.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5", "1.1.5" ] ], "tutorials": [ [ "ecology/ENA_Biodiv_submission", "Data submission using ENA upload Tool", "Ecology", "/topics/ecology/tutorials/ENA_Biodiv_submission/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/snpsift/snpSift_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1", "4.3+t.galaxy1" ] ], "tutorials": [ [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/bedtools/bedtools_getfastabed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0", "2.31.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1", "2.30.0+galaxy1" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/checkm_lineage_wf/checkm_lineage_wf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.4+galaxy2", "1.2.4+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.0+galaxy0", "1.2.0+galaxy0" ] ], "tutorials": [ [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ], [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/mothur_venn/mothur_venn": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_tree_shared/mothur_tree_shared": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_summary_single/mothur_summary_single": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2", "1.39.5.2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_sub_sample/mothur_sub_sample": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_remove_seqs/mothur_remove_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_remove_lineage/mothur_remove_lineage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_remove_groups/mothur_remove_groups": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_rarefaction_single/mothur_rarefaction_single": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_heatmap_sim/mothur_heatmap_sim": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_dist_shared/mothur_dist_shared": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_dist_seqs/mothur_dist_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_count_groups/mothur_count_groups": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_cluster/mothur_cluster": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "iuc/mothur_chimera_vsearch/mothur_chimera_vsearch": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1", "1.39.5.1" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "devteam/xy_plot/XY_Plot_1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2", "1.0.2" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ], [ "microbiome/mothur-miseq-sop-short", "16S Microbial Analysis with mothur (short)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html" ] ] }, "rnateam/sortmerna/bg_sortmerna": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0", "4.3.6+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/humann_unpack_pathways/humann_unpack_pathways": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.9+galaxy0", "3.9+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/humann_split_stratified_table/humann_split_stratified_table": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.9+galaxy0", "3.9+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/humann_renorm_table/humann_renorm_table": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.9+galaxy0", "3.9+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/humann_rename_table/humann_rename_table": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.9+galaxy0", "3.9+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/humann_regroup_table/humann_regroup_table": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.9+galaxy0", "3.9+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/humann/humann": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.9+galaxy0", "3.9+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/graphlan_annotate/graphlan_annotate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.1.3", "1.1.3" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/graphlan/graphlan": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.1.3", "1.1.3" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "iuc/export2graphlan/export2graphlan": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0", "0.20+galaxy0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ], [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "earlhaminst/lotus2/lotus2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0", "2.32+galaxy0" ] ], "tutorials": [ [ "microbiome/lotus2-identifying-fungi", "Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2", "Microbiome", "/topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0", "3.3.2.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ], [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ] ] }, "iuc/pe_histogram/pe_histogram": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.2", "1.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1", "1.0.1" ] ], "tutorials": [ [ "epigenetics/atac-seq", "ATAC-Seq data analysis", "Epigenetics", "/topics/epigenetics/tutorials/atac-seq/tutorial.html" ], [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ] ] }, "ecology/argo_getdata/argo_getdata": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0", "0.1.15+galaxy0" ] ], "tutorials": [ [ "climate/argo_pangeo", "Analyse Argo data", "Earth Data science", "/topics/climate/tutorials/argo_pangeo/tutorial.html" ], [ "climate/earth_system", "Getting your hands-on earth data", "Earth Data science", "/topics/climate/tutorials/earth_system/tutorial.html" ] ] }, "ecology/xarray_select/xarray_select": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1", "0.15.1" ] ], "tutorials": [ [ "climate/fates", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", "Earth Data science", "/topics/climate/tutorials/fates/tutorial.html" ], [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ] ] }, "ecology/xarray_mapplot/xarray_mapplot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0", "0.20.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0", "0.18.2+galaxy0" ] ], "tutorials": [ [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "ecology/x-array-map-plot", "Visualization of Climate Data using NetCDF xarray Map Plotting", "Ecology", "/topics/ecology/tutorials/x-array-map-plot/tutorial.html" ] ] }, "climate/climate_stripes/climate_stripes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1", "1.0.1" ] ], "tutorials": [ [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ], [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ] ] }, "bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1", "1.3.31+galaxy1" ] ], "tutorials": [ [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ], [ "ecology/x-array-map-plot", "Visualization of Climate Data using NetCDF xarray Map Plotting", "Ecology", "/topics/ecology/tutorials/x-array-map-plot/tutorial.html" ] ] }, "interactive_tool_copernicus_notebook": { "tool_id": [ [ "interactive_tool_copernicus_notebook", "interactive_tool_copernicus_notebook" ] ], "tutorials": [ [ "climate/sentinel5_data", "Sentinel 5P data visualisation", "Earth Data science", "/topics/climate/tutorials/sentinel5_data/tutorial.html" ], [ "ecology/ndvi_openeo", "From NDVI data with OpenEO to time series visualisation with Holoviews", "Ecology", "/topics/ecology/tutorials/ndvi_openeo/tutorial.html" ] ] }, "chemteam/gmx_solvate/gmx_solvate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.4+galaxy1", "2020.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.2+galaxy0", "2020.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4", "2019.1.4" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/md-simulation-gromacs", "Running molecular dynamics simulations using GROMACS", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html" ] ] }, "chemteam/gmx_sim/gmx_sim": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1", "2020.4+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0", "2020.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1", "2019.1.4.1" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/md-simulation-gromacs", "Running molecular dynamics simulations using GROMACS", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html" ] ] }, "chemteam/gmx_setup/gmx_setup": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.4+galaxy0", "2020.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.2+galaxy0", "2020.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4", "2019.1.4" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/md-simulation-gromacs", "Running molecular dynamics simulations using GROMACS", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html" ] ] }, "chemteam/gmx_em/gmx_em": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.4+galaxy0", "2020.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.2+galaxy0", "2020.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4", "2019.1.4" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/md-simulation-gromacs", "Running molecular dynamics simulations using GROMACS", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html" ] ] }, "chemteam/gmx_editconf/gmx_editconf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.4+galaxy0", "2020.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.2+galaxy0", "2020.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4", "2019.1.4" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ], [ "computational-chemistry/md-simulation-gromacs", "Running molecular dynamics simulations using GROMACS", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.html" ] ] }, "chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/1.0.0+galaxy0", "1.0.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.20", "0.20" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.19", "0.19" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ], [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "chemteam/bio3d_rmsf/bio3d_rmsf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3.4", "2.3.4" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3", "2.3" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ], [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "chemteam/bio3d_rmsd/bio3d_rmsd": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3.4", "2.3.4" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3", "2.3" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ], [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "chemteam/bio3d_pca/bio3d_pca": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3.4", "2.3.4" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3", "2.3" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ], [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "{{version_wc}}": { "tool_id": [ [ "{{version_wc}}", "{{version_wc}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_unique}}": { "tool_id": [ [ "{{version_unique}}", "{{version_unique}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_split}}": { "tool_id": [ [ "{{version_split}}", "{{version_split}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_sort}}": { "tool_id": [ [ "{{version_sort}}", "{{version_sort}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_select_first}}": { "tool_id": [ [ "{{version_select_first}}", "{{version_select_first}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_replace_text_line}}": { "tool_id": [ [ "{{version_replace_text_line}}", "{{version_replace_text_line}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_replace_text_column}}": { "tool_id": [ [ "{{version_replace_text_column}}", "{{version_replace_text_column}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_remove_columns_by_header}}": { "tool_id": [ [ "{{version_remove_columns_by_header}}", "{{version_remove_columns_by_header}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_remove_beginning}}": { "tool_id": [ [ "{{version_remove_beginning}}", "{{version_remove_beginning}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_paste}}": { "tool_id": [ [ "{{version_paste}}", "{{version_paste}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_join}}": { "tool_id": [ [ "{{version_join}}", "{{version_join}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_filter}}": { "tool_id": [ [ "{{version_filter}}", "{{version_filter}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_datamash}}": { "tool_id": [ [ "{{version_datamash}}", "{{version_datamash}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_cut_columns}}": { "tool_id": [ [ "{{version_cut_columns}}", "{{version_cut_columns}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_cut_advanced}}": { "tool_id": [ [ "{{version_cut_advanced}}", "{{version_cut_advanced}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_count}}": { "tool_id": [ [ "{{version_count}}", "{{version_count}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_compute}}": { "tool_id": [ [ "{{version_compute}}", "{{version_compute}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "{{version_cat}}": { "tool_id": [ [ "{{version_cat}}", "{{version_cat}}" ] ], "tutorials": [ [ "data-science/data-manipulation-olympics", "Data Manipulation Olympics", "Foundations of Data Science", "/topics/data-science/tutorials/data-manipulation-olympics/tutorial.html" ], [ "introduction/data-manipulation-olympics", "Data Manipulation Olympics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html" ] ] }, "bgruening/yolo_training/yolo_training": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/yolo_training/yolo_training/8.3.0+galaxy2", "8.3.0+galaxy2" ] ], "tutorials": [ [ "ecology/yolo_predict_deepsea", "Object detection with YOLO", "Ecology", "/topics/ecology/tutorials/yolo_predict_deepsea/tutorial.html" ], [ "imaging/yolo-segmentation-training", "Training Custom YOLO Models for Segmentation of Bioimages", "Imaging", "/topics/imaging/tutorials/yolo-segmentation-training/tutorial.html" ] ] }, "interactive_tool_anylabeling": { "tool_id": [ [ "interactive_tool_anylabeling", "interactive_tool_anylabeling" ] ], "tutorials": [ [ "ecology/SAM3", "SAM3 – AI-based Semantic Segmentation of marine biodiversity Images and Videos", "Ecology", "/topics/ecology/tutorials/SAM3/tutorial.html" ], [ "imaging/yolo-segmentation-training", "Training Custom YOLO Models for Segmentation of Bioimages", "Imaging", "/topics/imaging/tutorials/yolo-segmentation-training/tutorial.html" ] ] }, "imgteam/points2labelimage/ip_points_to_label": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/points2labelimage/ip_points_to_label/0.4.1+galaxy1", "0.4.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/points2labelimage/ip_points_to_label/0.4+galaxy0", "0.4+galaxy0" ] ], "tutorials": [ [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/electrophoresis-gel-bands-image-analysis", "Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools", "Imaging", "/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html" ] ] }, "imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.7.3+galaxy1", "0.7.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1-4", "0.0.1-4" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ], [ "imaging/hela-screen-analysis", "Analyse HeLa fluorescence siRNA screen", "Imaging", "/topics/imaging/tutorials/hela-screen-analysis/tutorial.html" ] ] }, "imgteam/spot_detection_2d/ip_spot_detection_2d": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d/0.1+galaxy0", "0.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d/0.0.1", "0.0.1" ] ], "tutorials": [ [ "imaging/2D-spot-detection", "Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines", "Imaging", "/topics/imaging/tutorials/2D-spot-detection/tutorial.html" ], [ "imaging/detection-of-mitoflashes", "Tracking of mitochondria and capturing mitoflashes", "Imaging", "/topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html" ] ] }, "imgteam/image_math/image_math": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/image_math/image_math/1.26.4+galaxy2", "1.26.4+galaxy2" ] ], "tutorials": [ [ "imaging/process-image-bioimageio", "Using BioImage.IO models for image analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/process-image-bioimageio/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ] ] }, "imgteam/count_objects/ip_count_objects": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2", "0.0.5-2" ] ], "tutorials": [ [ "imaging/imaging-introduction", "Introduction to Image Analysis using Galaxy", "Imaging", "/topics/imaging/tutorials/imaging-introduction/tutorial.html" ], [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ] ] }, "bgruening/cp_save_images/cp_save_images": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy2", "3.1.9+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy0", "3.1.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_measure_object_intensity/cp_measure_object_intensity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy0", "3.1.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_identify_primary_objects/cp_identify_primary_objects": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy2", "3.1.9+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy2", "3.1.9+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_common/cp_common": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9+galaxy2", "3.1.9+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_cellprofiler/cp_cellprofiler": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy0", "3.1.9+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "imgteam/color_deconvolution/ip_color_deconvolution": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/color_deconvolution/ip_color_deconvolution/0.9+galaxy0", "0.9+galaxy0" ] ], "tutorials": [ [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "bgruening/cp_overlay_outlines/cp_overlay_outlines": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy0", "3.1.9+galaxy0" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "bgruening/bioimage_inference/bioimage_inference": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/bioimage_inference/bioimage_inference/2.4.1+galaxy3", "2.4.1+galaxy3" ] ], "tutorials": [ [ "imaging/process-image-bioimageio", "Using BioImage.IO models for image analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/process-image-bioimageio/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "interactive_tool_qupath": { "tool_id": [ [ "interactive_tool_qupath", "interactive_tool_qupath" ] ], "tutorials": [ [ "imaging/electrophoresis-gel-bands-image-analysis", "Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools", "Imaging", "/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/tutorial.html" ], [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "peterjc/seq_filter_by_id/seq_filter_by_id": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9", "0.2.9" ], [ "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7", "0.2.7" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ], [ "single-cell/scrna-umis", "Understanding Barcodes", "Single Cell", "/topics/single-cell/tutorials/scrna-umis/tutorial.html" ] ] }, "bgruening/music_manipulate_eset/music_manipulate_eset": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4", "0.1.1+galaxy4" ] ], "tutorials": [ [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ], [ "single-cell/bulk-music-3-preparebulk", "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html" ] ] }, "ebi-gxa/scanpy_read_10x/scanpy_read_10x": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.9.3+galaxy0", "1.9.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ], [ "single-cell/bulk-music-2-preparescref", "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html" ] ] }, "ebi-gxa/monocle3_create/monocle3_create": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2", "0.1.4+galaxy2" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "ebi-gxa/dropletutils_read_10x/dropletutils_read_10x": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0", "1.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ], [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "bgruening/text_processing/tp_multijoin_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1", "9.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1", "1.1.1" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ], [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ] ] }, "bgruening/music_deconvolution/music_deconvolution": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4", "0.1.1+galaxy4" ] ], "tutorials": [ [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "single-cell/bulk-music", "Bulk RNA Deconvolution with MuSiC", "Single Cell", "/topics/single-cell/tutorials/bulk-music/tutorial.html" ] ] }, "iuc/seurat_reduce_dimension/seurat_reduce_dimension": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0", "5.0+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/seurat_preprocessing/seurat_preprocessing": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0", "5.0+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/seurat_plot/seurat_plot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0", "5.0+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/seurat_data/seurat_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0", "5.0+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/seurat_clustering/seurat_clustering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0", "5.0+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ], [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/dropletutils/dropletutils": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "1.10.0+galaxy2" ] ], "tutorials": [ [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ], [ "single-cell/scrna-preprocessing-tenx", "Pre-processing of 10X Single-Cell RNA Datasets", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html" ] ] }, "ebi-gxa/scanpy_run_umap/scanpy_run_umap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scanpy_parameter_iterator", "Scanpy Parameter Iterator", "Single Cell", "/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "ebi-gxa/scanpy_run_tsne/scanpy_run_tsne": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1", "1.8.1+galaxy1" ] ], "tutorials": [ [ "single-cell/scanpy_parameter_iterator", "Scanpy Parameter Iterator", "Single Cell", "/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html" ], [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "iuc/snapatac2_preprocessing/snapatac2_preprocessing": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1", "2.6.4+galaxy1" ] ], "tutorials": [ [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ] ] }, "iuc/snapatac2_plotting/snapatac2_plotting": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1", "2.6.4+galaxy1" ] ], "tutorials": [ [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ] ] }, "iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1", "2.6.4+galaxy1" ] ], "tutorials": [ [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ] ] }, "iuc/snapatac2_clustering/snapatac2_clustering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1", "2.6.4+galaxy1" ] ], "tutorials": [ [ "single-cell/scatac-batch-correction-snapatac2", "Multi-sample batch correction with Harmony and SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ] ] }, "bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2", "0.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1", "0.1" ] ], "tutorials": [ [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ], [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ] ] }, "bgruening/diff/diff": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.10+galaxy1", "3.10+galaxy1" ] ], "tutorials": [ [ "digital-humanities/introduction_to_dh", "Introduction to Digital Humanities in Galaxy", "Digital Humanities", "/topics/digital-humanities/tutorials/introduction_to_dh/tutorial.html" ], [ "digital-humanities/text_mining_chinese", "Text-Mining Differences in Chinese Newspaper Articles", "Digital Humanities", "/topics/digital-humanities/tutorials/text_mining_chinese/tutorial.html" ] ] }, "interactive_tool_openrefine": { "tool_id": [ [ "interactive_tool_openrefine", "interactive_tool_openrefine" ] ], "tutorials": [ [ "digital-humanities/open-refine-tutorial", "OpenRefine Tutorial for researching cultural data", "Digital Humanities", "/topics/digital-humanities/tutorials/open-refine-tutorial/tutorial.html" ], [ "ecology/openrefine_gbif", "Cleaning GBIF data using OpenRefine", "Ecology", "/topics/ecology/tutorials/openrefine_gbif/tutorial.html" ] ] }, "galaxyp/metanovo/metanovo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4", "1.9.4+galaxy4" ] ], "tutorials": [ [ "microbiome/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-1-database-generation/tutorial.html" ], [ "proteomics/clinical-mp-1-database-generation", "Clinical Metaproteomics 1: Database-Generation", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html" ] ] }, "galaxyp/peptideshaker/fasta_cli": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/fasta_cli/4.0.41+galaxy1", "4.0.41+galaxy1" ] ], "tutorials": [ [ "microbiome/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Microbiome", "/topics/microbiome/tutorials/clinical-mp-2-discovery/tutorial.html" ], [ "proteomics/clinical-mp-2-discovery", "Clinical Metaproteomics 2: Discovery", "Proteomics", "/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html" ] ] }, "galaxyp/openms_xtandemadapter/XTandemAdapter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1", "2.2.0.1" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_textexporter/TextExporter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0", "2.6+galaxy0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_peptideindexer/PeptideIndexer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_idscoreswitcher/IDScoreSwitcher": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy", "2.6+galaxy" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_fileinfo/FileInfo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_fidoadapter/FidoAdapter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1", "2.2.0.1" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ], [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/ml-modeling-of-anti-cancer-peptides", "Machine Learning Modeling of Anticancer Peptides", "Proteomics", "/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html" ], [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "jay/pdaug_merge_dataframes/pdaug_merge_dataframes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/ml-modeling-of-anti-cancer-peptides", "Machine Learning Modeling of Anticancer Peptides", "Proteomics", "/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html" ], [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "jay/pdaug_basic_plots/pdaug_basic_plots": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/ml-modeling-of-anti-cancer-peptides", "Machine Learning Modeling of Anticancer Peptides", "Proteomics", "/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html" ], [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "jay/pdaug_addclasslabel/pdaug_addclasslabel": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/ml-modeling-of-anti-cancer-peptides", "Machine Learning Modeling of Anticancer Peptides", "Proteomics", "/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html" ], [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "proteore/proteore_venn_diagram/Jvenn": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21", "2019.02.21" ], [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2018.12.18", "2018.12.18" ] ], "tutorials": [ [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ], [ "proteomics/proteome_annotation", "Annotating a protein list identified by LC-MS/MS experiments", "Proteomics", "/topics/proteomics/tutorials/proteome_annotation/tutorial.html" ] ] }, "proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27", "2019.02.27" ] ], "tutorials": [ [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ], [ "proteomics/proteome_annotation", "Annotating a protein list identified by LC-MS/MS experiments", "Proteomics", "/topics/proteomics/tutorials/proteome_annotation/tutorial.html" ] ] }, "proteore/proteore_id_converter/IDconverter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07", "2019.03.07" ], [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.01.28", "2019.01.28" ] ], "tutorials": [ [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ], [ "proteomics/proteome_annotation", "Annotating a protein list identified by LC-MS/MS experiments", "Proteomics", "/topics/proteomics/tutorials/proteome_annotation/tutorial.html" ] ] }, "proteore/proteore_expression_rnaseq_abbased/rna_abbased_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07", "2019.03.07" ] ], "tutorials": [ [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ], [ "proteomics/proteome_annotation", "Annotating a protein list identified by LC-MS/MS experiments", "Proteomics", "/topics/proteomics/tutorials/proteome_annotation/tutorial.html" ] ] }, "galaxyp/metaquantome_viz/metaquantome_viz": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0", "2.0.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0", "2.0.0-0" ] ], "tutorials": [ [ "proteomics/metaquantome-function", "metaQuantome 2: Function", "Proteomics", "/topics/proteomics/tutorials/metaquantome-function/tutorial.html" ], [ "proteomics/metaquantome-taxonomy", "metaQuantome 3: Taxonomy", "Proteomics", "/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html" ] ] }, "galaxyp/metaquantome_stat/metaquantome_stat": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0", "2.0.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0", "2.0.0-0" ] ], "tutorials": [ [ "proteomics/metaquantome-function", "metaQuantome 2: Function", "Proteomics", "/topics/proteomics/tutorials/metaquantome-function/tutorial.html" ], [ "proteomics/metaquantome-taxonomy", "metaQuantome 3: Taxonomy", "Proteomics", "/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html" ] ] }, "galaxyp/metaquantome_sample/metaquantome_sample": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0", "2.0.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0", "2.0.0-0" ] ], "tutorials": [ [ "proteomics/metaquantome-function", "metaQuantome 2: Function", "Proteomics", "/topics/proteomics/tutorials/metaquantome-function/tutorial.html" ], [ "proteomics/metaquantome-taxonomy", "metaQuantome 3: Taxonomy", "Proteomics", "/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html" ] ] }, "galaxyp/metaquantome_filter/metaquantome_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0", "2.0.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0", "2.0.0-0" ] ], "tutorials": [ [ "proteomics/metaquantome-function", "metaQuantome 2: Function", "Proteomics", "/topics/proteomics/tutorials/metaquantome-function/tutorial.html" ], [ "proteomics/metaquantome-taxonomy", "metaQuantome 3: Taxonomy", "Proteomics", "/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html" ] ] }, "galaxyp/metaquantome_expand/metaquantome_expand": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0", "2.0.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0", "2.0.0-0" ] ], "tutorials": [ [ "proteomics/metaquantome-function", "metaQuantome 2: Function", "Proteomics", "/topics/proteomics/tutorials/metaquantome-function/tutorial.html" ], [ "proteomics/metaquantome-taxonomy", "metaQuantome 3: Taxonomy", "Proteomics", "/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html" ] ] }, "galaxyp/metaquantome_db/metaquantome_db": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0", "2.0.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0", "2.0.0-0" ] ], "tutorials": [ [ "proteomics/metaquantome-function", "metaQuantome 2: Function", "Proteomics", "/topics/proteomics/tutorials/metaquantome-function/tutorial.html" ], [ "proteomics/metaquantome-taxonomy", "metaQuantome 3: Taxonomy", "Proteomics", "/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html" ] ] }, "iuc/sqlite_to_tabular/sqlite_to_tabular": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1", "3.2.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0", "2.0.0" ] ], "tutorials": [ [ "proteomics/metaproteomics", "Metaproteomics tutorial", "Proteomics", "/topics/proteomics/tutorials/metaproteomics/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "galaxyp/translate_bed/translate_bed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "galaxyp/gffcompare_to_bed/gffcompare_to_bed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1", "0.2.1" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "galaxyp/custom_pro_db/custom_pro_db": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0", "1.22.0" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "galaxyp/bed_to_protein_map/bed_to_protein_map": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0", "0.2.0" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "bgruening/column_regex_find_replace/column_regex_find_and_replace": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/column_regex_find_replace/column_regex_find_and_replace/1.0.3", "1.0.3" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ], [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ] ] }, "comp1": { "tool_id": [ [ "comp1", "comp1" ] ], "tutorials": [ [ "introduction/galaxy-intro-101", "Galaxy Basics for genomics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-101/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ] ] }, "galaxyp/pep_pointer/pep_pointer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3+galaxy1", "0.1.3+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3", "0.1.3" ] ], "tutorials": [ [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ], [ "proteomics/proteogenomics-novel-peptide-analysis", "Proteogenomics 3: Novel peptide analysis", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html" ] ] }, "bgruening/uniprot_rest_interface/uniprot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.7", "0.7" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.5", "0.5" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1", "0.1" ] ], "tutorials": [ [ "proteomics/maxquant-msstats-dda-lfq", "MaxQuant and MSstats for the analysis of label-free data", "Proteomics", "/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html" ], [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ] ] }, "nml/staramr/staramr_search": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2", "0.7.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1", "0.5.1" ], [ "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1", "0.10.0+galaxy1" ] ], "tutorials": [ [ "genome-annotation/amr-gene-detection", "Identification of AMR genes in an assembled bacterial genome", "Genome Annotation", "/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html" ], [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "bgruening/natural_product_likeness/ctb_np-likeness-calculator": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1", "2.1" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "bgruening/chemfp/ctb_chemfp_mol2fps": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5", "1.5" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0", "0.2.0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ], [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "iuc/funannotate_predict/funannotate_predict": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2", "1.8.9+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy1", "1.8.15+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0", "1.8.15+galaxy0" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ] ] }, "galaxyp/eggnog_mapper/eggnog_mapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3", "2.1.8+galaxy3" ] ], "tutorials": [ [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ], [ "genome-annotation/functional", "Functional annotation of protein sequences", "Genome Annotation", "/topics/genome-annotation/tutorials/functional/tutorial.html" ] ] }, "iuc/tbl2gff3/tbl2gff3": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2", "1.2" ] ], "tutorials": [ [ "genome-annotation/amr-gene-detection", "Identification of AMR genes in an assembled bacterial genome", "Genome Annotation", "/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html" ], [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ] ] }, "gga/apollo_iframe/iframe": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5", "4.2.5" ] ], "tutorials": [ [ "genome-annotation/apollo", "Refining Genome Annotations with Apollo (prokaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo/tutorial.html" ], [ "genome-annotation/apollo-euk", "Refining Genome Annotations with Apollo (eukaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo-euk/tutorial.html" ] ] }, "gga/apollo_create_or_update/create_or_update": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5", "4.2.5" ] ], "tutorials": [ [ "genome-annotation/apollo", "Refining Genome Annotations with Apollo (prokaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo/tutorial.html" ], [ "genome-annotation/apollo-euk", "Refining Genome Annotations with Apollo (eukaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo-euk/tutorial.html" ] ] }, "iuc/bedtools/bedtools_maskfastabed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1", "2.31.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0", "2.30.0" ] ], "tutorials": [ [ "genome-annotation/repeatmasker", "Masking repeats with RepeatMasker", "Genome Annotation", "/topics/genome-annotation/tutorials/repeatmasker/tutorial.html" ], [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "bgruening/repeat_masker/repeatmasker_wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0", "4.1.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0", "4.1.2-p1+galaxy0" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ], [ "genome-annotation/repeatmasker", "Masking repeats with RepeatMasker", "Genome Annotation", "/topics/genome-annotation/tutorials/repeatmasker/tutorial.html" ] ] }, "iuc/braker3/braker3": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/braker3/braker3/3.0.8+galaxy0", "3.0.8+galaxy0" ] ], "tutorials": [ [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ], [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ] ] }, "genouest/helixer/helixer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1", "0.3.3+galaxy1" ] ], "tutorials": [ [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ], [ "genome-annotation/helixer", "Genome annotation with Helixer", "Genome Annotation", "/topics/genome-annotation/tutorials/helixer/tutorial.html" ] ] }, "genouest/braker3/braker3": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.8+galaxy0", "3.0.8+galaxy0" ] ], "tutorials": [ [ "genome-annotation/braker3", "Genome annotation with Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/braker3/tutorial.html" ], [ "genome-annotation/comparison-braker-helixer-annotation", "Comparison of two annotation tools - Helixer and Braker3", "Genome Annotation", "/topics/genome-annotation/tutorials/comparison-braker-helixer-annotation/tutorial.html" ] ] }, "iuc/maker_map_ids/maker_map_ids": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11", "2.31.11" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10", "2.31.10" ] ], "tutorials": [ [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ], [ "genome-annotation/annotation-with-maker-short", "Genome annotation with Maker (short)", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html" ] ] }, "iuc/maker/maker": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11", "2.31.11" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10", "2.31.10" ] ], "tutorials": [ [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ], [ "genome-annotation/annotation-with-maker-short", "Genome annotation with Maker (short)", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html" ] ] }, "Show tail1": { "tool_id": [ [ "Show tail1", "Show tail1" ] ], "tutorials": [ [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ], [ "transcriptomics/rna-seq-viz-with-heatmap2", "Visualization of RNA-Seq results with heatmap2", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html" ] ] }, "iuc/meme_chip/meme_chip": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1", "4.11.2+galaxy1" ] ], "tutorials": [ [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "iuc/extract_genomic_dna/Extract genomic DNA 1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy3", "3.0.3+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2", "3.0.3+galaxy2" ] ], "tutorials": [ [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ], [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "bgruening/salmon/salmon": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2", "1.10.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2", "0.8.2" ] ], "tutorials": [ [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ], [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ] ] }, "devteam/samtools_sort/samtools_sort": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.7", "2.0.7" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2", "2.0.2" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ], [ "transcriptomics/small_ncrna_clustering", "Small Non-coding RNA Clustering using BlockClust", "Transcriptomics", "/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html" ] ] }, "ethevenot/multivariate/Multivariate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10", "2.3.10" ] ], "tutorials": [ [ "metabolomics/lcms-dataprocessing", "Mass spectrometry: LC-MS data processing", "Metabolomics", "/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ] ] }, "iuc/stringtie/stringtie_merge": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0", "2.2.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.6", "1.3.6" ] ], "tutorials": [ [ "transcriptomics/de-novo", "De novo transcriptome reconstruction with RNA-Seq", "Transcriptomics", "/topics/transcriptomics/tutorials/de-novo/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "gene2exon1": { "tool_id": [ [ "gene2exon1", "gene2exon1" ] ], "tutorials": [ [ "introduction/galaxy-intro-strands", "Introduction to Genomics and Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html" ], [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/goenrichment/goenrichment": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1", "2.0.1" ] ], "tutorials": [ [ "single-cell/GO-enrichment", "GO Enrichment Analysis on Single-Cell RNA-Seq Data", "Single Cell", "/topics/single-cell/tutorials/GO-enrichment/tutorial.html" ], [ "transcriptomics/goenrichment", "GO Enrichment Analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/goenrichment/tutorial.html" ] ] }, "iuc/limma_voom/limma_voom": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0", "3.50.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9", "3.34.9.9" ] ], "tutorials": [ [ "transcriptomics/minerva-pathways", "Pathway analysis with the MINERVA Platform", "Transcriptomics", "/topics/transcriptomics/tutorials/minerva-pathways/tutorial.html" ], [ "transcriptomics/rna-seq-counts-to-genes", "2: RNA-seq counts to genes", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html" ] ] }, "nml/metaspades/metaspades": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.2.0+galaxy0", "4.2.0+galaxy0" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "iuc/ngsutils_bam_filter/ngsutils_bam_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9", "0.5.9" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "iuc/megahit_contig2fastg/megahit_contig2fastg": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10", "1.1.3+galaxy10" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1", "1.1.3+galaxy1" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "iuc/megahit/megahit": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2", "1.2.9+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0", "1.2.9+galaxy0" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "iuc/coverm_contig/coverm_contig": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0", "0.7.0+galaxy0" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "devteam/bamtools/bamtools": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0", "2.5.1+galaxy0" ] ], "tutorials": [ [ "assembly/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Assembly", "/topics/assembly/tutorials/metagenomics-assembly/tutorial.html" ], [ "microbiome/metagenomics-assembly", "Assembly of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-assembly/tutorial.html" ] ] }, "iuc/chromeister/chromeister": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1", "1.5.a+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a", "1.5.a" ] ], "tutorials": [ [ "assembly/assembly-quality-control", "Genome Assembly Quality Control", "Assembly", "/topics/assembly/tutorials/assembly-quality-control/tutorial.html" ], [ "genome-annotation/hpc-for-lsgc", "From small to large-scale genome comparison", "Genome Annotation", "/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html" ] ] }, "iuc/medaka_consensus_pipeline/medaka_consensus_pipeline": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1", "1.7.2+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0", "1.7.2+galaxy0" ] ], "tutorials": [ [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "bgruening/racon/racon": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1", "1.5.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13", "1.4.13" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1", "1.3.1.1" ] ], "tutorials": [ [ "assembly/largegenome", "Large genome assembly and polishing", "Assembly", "/topics/assembly/tutorials/largegenome/tutorial.html" ], [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "bgruening/hifiasm/hifiasm": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0", "0.25.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0", "0.19.8+galaxy0" ] ], "tutorials": [ [ "assembly/hifi-assembly", "Genome assembly using PacBio data", "Assembly", "/topics/assembly/tutorials/hifi-assembly/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "iuc/pretext_snapshot/pretext_snapshot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "0.0.3+galaxy1" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "iuc/pretext_map/pretext_map": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1", "0.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", "0.1.9+galaxy0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "iuc/bellerophon/bellerophon": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "1.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0", "1.0+galaxy0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ], [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "devteam/fasta_filter_by_length/fasta_filter_by_length": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2", "1.2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", "1.1" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ], [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ] ] }, "iuc/pilon/pilon": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1", "1.20.1" ] ], "tutorials": [ [ "assembly/chloroplast-assembly", "Chloroplast genome assembly", "Assembly", "/topics/assembly/tutorials/chloroplast-assembly/tutorial.html" ], [ "assembly/hybrid_denovo_assembly", "Hybrid genome assembly - Nanopore and Illumina", "Assembly", "/topics/assembly/tutorials/hybrid_denovo_assembly/tutorial.html" ] ] }, "goeckslab/image_learner/image_learner": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/image_learner/image_learner/0.1.5", "0.1.5" ] ], "tutorials": [ [ "statistics/GTEx_Tissue_modeling", "GTEx Tissue Modeling with Galaxy Image Learner", "Statistics and machine learning", "/topics/statistics/tutorials/GTEx_Tissue_modeling/tutorial.html" ], [ "statistics/image_learner", "GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000", "Statistics and machine learning", "/topics/statistics/tutorials/image_learner/tutorial.html" ] ] }, "interactive_tool_ml_jupyter_notebook": { "tool_id": [ [ "interactive_tool_ml_jupyter_notebook", "interactive_tool_ml_jupyter_notebook" ] ], "tutorials": [ [ "statistics/fine_tuning_protTrans", "Fine tune large protein model (ProtTrans) using HuggingFace", "Statistics and machine learning", "/topics/statistics/tutorials/fine_tuning_protTrans/tutorial.html" ], [ "statistics/gpu_jupyter_lab", "A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy", "Statistics and machine learning", "/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html" ] ] }, "bgruening/sklearn_to_categorical/sklearn_to_categorical": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3", "1.0.8.3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.10.0", "1.0.10.0" ] ], "tutorials": [ [ "statistics/CNN", "Deep Learning (Part 3) - Convolutional neural networks (CNN)", "Statistics and machine learning", "/topics/statistics/tutorials/CNN/tutorial.html" ], [ "statistics/fruit_360", "Image classification in Galaxy with fruit 360 dataset", "Statistics and machine learning", "/topics/statistics/tutorials/fruit_360/tutorial.html" ] ] }, "bgruening/flexynesis_utils/flexynesis_utils": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_utils/flexynesis_utils/0.2.20+galaxy3", "0.2.20+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_utils/flexynesis_utils/0.2.20+galaxy2", "0.2.20+galaxy2" ] ], "tutorials": [ [ "statistics/flexynesis_cbio_import", "Prepare Data from CbioPortal for Flexynesis Integration", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html" ], [ "statistics/flexynesis_unsupervised", "Unsupervised Analysis of Bone Marrow Cells with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_unsupervised/tutorial.html" ] ] }, "bgruening/sklearn_generalized_linear/sklearn_generalized_linear": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.11.2", "1.0.11.2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.11.0", "1.0.11.0" ] ], "tutorials": [ [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ], [ "statistics/regression_machinelearning", "Regression in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/regression_machinelearning/tutorial.html" ] ] }, "devteam/bam_to_sam/bam_to_sam": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1", "2.0.1" ] ], "tutorials": [ [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ], [ "epigenetics/estrogen-receptor-binding-site-identification", "Identification of the binding sites of the Estrogen receptor", "Epigenetics", "/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html" ] ] }, "climate/c3s/c3s": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.2.0", "0.2.0" ], [ "toolshed.g2.bx.psu.edu/repos/climate/c3s/c3s/0.1.0", "0.1.0" ] ], "tutorials": [ [ "climate/earth_system", "Getting your hands-on earth data", "Earth Data science", "/topics/climate/tutorials/earth_system/tutorial.html" ], [ "contributing/create-new-tutorial", "Creating a new tutorial", "Contributing to the Galaxy Training Material", "/topics/contributing/tutorials/create-new-tutorial/tutorial.html" ] ] }, "__FILTER_FAILED_DATASETS__": { "tool_id": [ [ "__FILTER_FAILED_DATASETS__", "__FILTER_FAILED_DATASETS__" ] ], "tutorials": [ [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ], [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "melpetera/generic_filter/generic_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2020.01", "2020.01" ], [ "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2017.04", "2017.04" ] ], "tutorials": [ [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-dataprocessing", "Mass spectrometry: LC-MS data processing", "Metabolomics", "/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html" ] ] }, "melpetera/batchcorrection/Batch_correction": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0", "3.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/2.1.2", "2.1.2" ] ], "tutorials": [ [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-dataprocessing", "Mass spectrometry: LC-MS data processing", "Metabolomics", "/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html" ] ] }, "lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.7+camera1.48.0-galaxy1", "2.2.7+camera1.48.0-galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.6+camera1.48.0-galaxy0", "2.2.6+camera1.48.0-galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.4", "2.2.4" ] ], "tutorials": [ [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "ethevenot/qualitymetrics/quality_metrics": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8", "2.2.8" ] ], "tutorials": [ [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ], [ "metabolomics/lcms-dataprocessing", "Mass spectrometry: LC-MS data processing", "Metabolomics", "/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html" ] ] }, "galaxyp/cardinal_mz_images/cardinal_mz_images": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.2", "2.6.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0", "2.6.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2", "1.12.1.2" ] ], "tutorials": [ [ "metabolomics/msi-analyte-distribution", "Mass spectrometry imaging: Examining the spatial distribution of analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html" ], [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "galaxyp/cardinal_data_exporter/cardinal_data_exporter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0", "2.6.0.0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1", "1.12.1.1" ] ], "tutorials": [ [ "metabolomics/msi-analyte-distribution", "Mass spectrometry imaging: Examining the spatial distribution of analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html" ], [ "proteomics/mass-spectrometry-imaging-loading-exploring-data", "Mass spectrometry imaging: Loading and exploring MSI data", "Proteomics", "/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html" ] ] }, "CONVERTER_uncompressed_to_gz": { "tool_id": [ [ "CONVERTER_uncompressed_to_gz", "CONVERTER_uncompressed_to_gz" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/lofreq_viterbi/lofreq_viterbi": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0", "2.1.5+galaxy0" ] ], "tutorials": [ [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "iuc/lofreq_indelqual/lofreq_indelqual": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1", "2.1.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0", "2.1.5+galaxy0" ] ], "tutorials": [ [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ], [ "variant-analysis/sars-cov-2", "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2/tutorial.html" ] ] }, "iuc/ivar_consensus/ivar_consensus": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.3+galaxy0", "1.4.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0", "1.4.2+galaxy0" ] ], "tutorials": [ [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ], [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "bgruening/column_arrange_by_header/bg_column_arrange_by_header": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2", "0.2" ] ], "tutorials": [ [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "devteam/picard/picard_MergeSamFiles": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0", "3.1.1.0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1", "2.18.2.1" ] ], "tutorials": [ [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ] ] }, "iuc/sra_tools/fastq_dump": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.1.1+galaxy1", "3.1.1+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0", "2.11.0+galaxy0" ] ], "tutorials": [ [ "galaxy-interface/ncbi-sarf", "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ] ] }, "iuc/ncbi_acc_download/ncbi_acc_download": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0", "0.2.8+galaxy0" ] ], "tutorials": [ [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ], [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ] ] }, "devteam/vcf2tsv/vcf2tsv": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0", "1.0.0_rc3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0", "1.0.0_rc1+galaxy0" ] ], "tutorials": [ [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ], [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ] ] }, "iuc/gemini_query/gemini_query": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy2", "0.20.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1", "0.20.1+galaxy1" ] ], "tutorials": [ [ "variant-analysis/dip", "Calling variants in diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/dip/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "iuc/snpeff/snpEff_download": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/5.2+galaxy1", "5.2+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0", "4.1.0" ] ], "tutorials": [ [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ] ] }, "iuc/gemini_inheritance/gemini_inheritance": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1", "0.20.1" ] ], "tutorials": [ [ "variant-analysis/exome-seq", "Exome sequencing data analysis for diagnosing a genetic disease", "Variant Analysis", "/topics/variant-analysis/tutorials/exome-seq/tutorial.html" ], [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/tbprofiler/tb_profiler_profile": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.6.4+galaxy0", "6.6.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0", "3.0.8+galaxy0" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/tb_variant_filter/tb_variant_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0", "0.4.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.6+galaxy0", "0.3.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2", "0.3.5+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0", "0.1.3+galaxy0" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ], [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "mbernt/fasta_regex_finder/fasta_regex_finder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0", "0.1.0" ] ], "tutorials": [ [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ], [ "variant-analysis/sars-cov-2-variant-discovery", "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html" ] ] }, "iuc/pangolin/pangolin": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3+galaxy2", "4.3+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8", "2.3.8" ] ], "tutorials": [ [ "galaxy-interface/workflow-automation", "Automating Galaxy workflows using the command line", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-automation/tutorial.html" ], [ "variant-analysis/sars-cov-2-variant-discovery", "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html" ] ] }, "devteam/samtools_calmd/samtools_calmd": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.3", "2.0.3" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2", "2.0.2" ] ], "tutorials": [ [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ], [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker/1.1.4+galaxy0", "1.1.4+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/med-chem-data", "Data management in Medicinal Chemistry", "Computational chemistry", "/topics/computational-chemistry/tutorials/med-chem-data/tutorial.html" ], [ "fair/med-chem-data", "Data management in Medicinal Chemistry", "FAIR Data, Workflows, and Research", "/topics/fair/tutorials/med-chem-data/tutorial.html" ] ] }, "iuc/length_and_gc_content/length_and_gc_content": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2", "0.1.2" ] ], "tutorials": [ [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ] ] }, "iuc/gtftobed12/gtftobed12": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357", "357" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ], [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "iuc/deg_annotate/deg_annotate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0+galaxy1", "1.1.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0", "1.1.0" ] ], "tutorials": [ [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ], [ "transcriptomics/rna-seq-analysis-clustering-viz", "RNA-Seq data analysis, clustering and visualisation tutorial", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/tutorial.html" ] ] }, "bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "0.4" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1", "0.1" ] ], "tutorials": [ [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ], [ "statistics/classification_regression", "Machine learning: classification and regression", "Statistics and machine learning", "/topics/statistics/tutorials/classification_regression/tutorial.html" ] ] }, "devteam/velvet/velveth": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.3", "1.2.10.3" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.1", "1.2.10.1" ] ], "tutorials": [ [ "assembly/debruijn-graph-assembly", "De Bruijn Graph Assembly", "Assembly", "/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html" ], [ "assembly/general-introduction", "An Introduction to Genome Assembly", "Assembly", "/topics/assembly/tutorials/general-introduction/tutorial.html" ] ] }, "devteam/velvet/velvetg": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.2", "1.2.10.2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.1", "1.2.10.1" ] ], "tutorials": [ [ "assembly/debruijn-graph-assembly", "De Bruijn Graph Assembly", "Assembly", "/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html" ], [ "assembly/general-introduction", "An Introduction to Genome Assembly", "Assembly", "/topics/assembly/tutorials/general-introduction/tutorial.html" ] ] }, "iuc/mothur_merge_files/mothur_merge_files": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "iuc/mothur_make_biom/mothur_make_biom": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ] ] }, "iuc/mothur_align_seqs/mothur_align_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0", "1.39.5.0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ], [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ] ] }, "devteam/ncbi_blast_plus/ncbi_blastx_wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/2.10.1+galaxy2", "2.10.1+galaxy2" ] ], "tutorials": [ [ "sequence-analysis/ncbi-blast-against-the-madland", "NCBI BLAST+ against the MAdLand", "Sequence analysis", "/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html" ] ] }, "interactive_tool_qgis": { "tool_id": [ [ "interactive_tool_qgis", "interactive_tool_qgis" ] ], "tutorials": [ [ "ecology/QGIS_Web_Feature_Services", "QGIS Web Feature Services", "Ecology", "/topics/ecology/tutorials/QGIS_Web_Feature_Services/tutorial.html" ] ] }, "bgruening/kmetashot/kmetashot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/kmetashot/kmetashot/2.0+galaxy2", "2.0+galaxy2" ] ], "tutorials": [ [ "microbiome/mags-building", "Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads", "Microbiome", "/topics/microbiome/tutorials/mags-building/tutorial.html" ] ] }, "bgruening/edit_coco_annotation/edit_coco_annotation": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/edit_coco_annotation/edit_coco_annotation/1.0.0+galaxy0", "1.0.0+galaxy0" ] ], "tutorials": [ [ "imaging/Annotation_AI_Pipeline", "AI pipeline for annotating marine species (Project Moorev - Marine)", "Imaging", "/topics/imaging/tutorials/Annotation_AI_Pipeline/tutorial.html" ] ] }, "bgruening/coco_annotation_visualizer/coco_annotation_visualizer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/coco_annotation_visualizer/coco_annotation_visualizer/1.0.0", "1.0.0" ] ], "tutorials": [ [ "imaging/Annotation_AI_Pipeline", "AI pipeline for annotating marine species (Project Moorev - Marine)", "Imaging", "/topics/imaging/tutorials/Annotation_AI_Pipeline/tutorial.html" ] ] }, "iuc/tesseract/tesseract": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/tesseract/tesseract/5.5.2+galaxy4", "5.5.2+galaxy4" ] ], "tutorials": [ [ "digital-humanities/grobid", "Text-Mining articles with GROBID", "Digital Humanities", "/topics/digital-humanities/tutorials/grobid/tutorial.html" ] ] }, "iuc/grobid_grobid/grobid_grobid": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/grobid_grobid/grobid_grobid/0.9.0+galaxy0", "0.9.0+galaxy0" ] ], "tutorials": [ [ "digital-humanities/grobid", "Text-Mining articles with GROBID", "Digital Humanities", "/topics/digital-humanities/tutorials/grobid/tutorial.html" ] ] }, "iuc/grobid_dataset_annotate/grobid_dataset_annotate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/grobid_dataset_annotate/grobid_dataset_annotate/0.8.1+galaxy0", "0.8.1+galaxy0" ] ], "tutorials": [ [ "digital-humanities/grobid", "Text-Mining articles with GROBID", "Digital Humanities", "/topics/digital-humanities/tutorials/grobid/tutorial.html" ] ] }, "iuc/ppanggolin_msa/ppanggolin_msa": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ppanggolin_msa/ppanggolin_msa/2.2.1+galaxy1", "2.2.1+galaxy1" ] ], "tutorials": [ [ "genome-annotation/bacterial-pangenomics", "Bacterial pangenomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html" ] ] }, "iuc/ppanggolin_all/ppanggolin_all": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ppanggolin_all/ppanggolin_all/2.2.1+galaxy1", "2.2.1+galaxy1" ] ], "tutorials": [ [ "genome-annotation/bacterial-pangenomics", "Bacterial pangenomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html" ] ] }, "iuc/ncbi_datasets/datasets_download_genome": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome/16.42.0+galaxy0", "16.42.0+galaxy0" ] ], "tutorials": [ [ "genome-annotation/bacterial-comparative-genomics-dataset-construction", "Dataset construction for bacterial comparative genomics", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/tutorial.html" ] ] }, "iuc/roary/roary": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0+galaxy3", "3.13.0+galaxy3" ] ], "tutorials": [ [ "genome-annotation/pangenome-annotation-with-roary", "Pangenome analysis with Roary", "Genome Annotation", "/topics/genome-annotation/tutorials/pangenome-annotation-with-roary/tutorial.html" ] ] }, "iuc/checkm2/checkm2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy0", "1.0.2+galaxy0" ] ], "tutorials": [ [ "genome-annotation/bacterial-genome-quality-control", "Bacterial genome quality control", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-quality-control/tutorial.html" ] ] }, "iuc/chopin2/chopin2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/chopin2/chopin2/1.0.7+galaxy1", "1.0.7+galaxy1" ] ], "tutorials": [ [ "statistics/hyperdimensional_computing", "Supervised Learning with Hyperdimensional Computing", "Statistics and machine learning", "/topics/statistics/tutorials/hyperdimensional_computing/tutorial.html" ] ] }, "marie-tremblay-metatoul/normalization/normalization": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/normalization/normalization/1.0.7", "1.0.7" ] ], "tutorials": [ [ "metabolomics/lcms-dataprocessing", "Mass spectrometry: LC-MS data processing", "Metabolomics", "/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html" ] ] }, "yguitton/metams_rungc/metams_runGC": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/yguitton/metams_rungc/metams_runGC/3.0.0+metaMS1.24.0-galaxy0", "3.0.0+metaMS1.24.0-galaxy0" ] ], "tutorials": [ [ "metabolomics/gcms", "Mass spectrometry: GC-MS analysis with the metaMS package", "Metabolomics", "/topics/metabolomics/tutorials/gcms/tutorial.html" ] ] }, "iuc/cnv_vcf2json/cnv_vcf2json": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/cnv_vcf2json/cnv_vcf2json/1.1.o+galaxy0.1", "1.1.o+galaxy0.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/cnv_vcf2json/cnv_vcf2json/1.1.0+galaxy0.1", "1.1.0+galaxy0.1" ] ], "tutorials": [ [ "variant-analysis/beaconise_1000hg", "Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons", "Variant Analysis", "/topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html" ] ] }, "iuc/cnv_phenopacket/cnv_phenopacket": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/cnv_phenopacket/cnv_phenopacket/1.0.2+galaxy0", "1.0.2+galaxy0" ] ], "tutorials": [ [ "variant-analysis/beaconise_1000hg", "Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons", "Variant Analysis", "/topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html" ] ] }, "iuc/beacon2_import/beacon2_import": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/beacon2_import/beacon2_import/2.1.1+galaxy0", "2.1.1+galaxy0" ] ], "tutorials": [ [ "variant-analysis/beaconise_1000hg", "Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons", "Variant Analysis", "/topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.html" ] ] }, "iuc/vapor/vapor": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy3", "1.0.2+galaxy3" ] ], "tutorials": [ [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ] ] }, "iuc/bamtools_split_ref/bamtools_split_ref": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy2", "2.5.2+galaxy2" ] ], "tutorials": [ [ "variant-analysis/aiv-analysis", "Avian influenza viral strain analysis from gene segment sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/aiv-analysis/tutorial.html" ] ] }, "iuc/countess/countess": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/countess/countess/0.1.26+galaxy0", "0.1.26+galaxy0" ] ], "tutorials": [ [ "variant-analysis/countess-mave-chek2", "Calculating CHEK2 variant effect scores from MAVE data with CountESS", "Variant Analysis", "/topics/variant-analysis/tutorials/countess-mave-chek2/tutorial.html" ] ] }, "iuc/jq/jq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0", "1.0" ] ], "tutorials": [ [ "galaxy-interface/ncbi-sarf", "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html" ] ] }, "devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4", "0.0.4" ] ], "tutorials": [ [ "admin/reference-genomes", "Reference Data with Data Managers", "Galaxy Server administration", "/topics/admin/tutorials/reference-genomes/tutorial.html" ] ] }, "devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.5", "0.0.5" ] ], "tutorials": [ [ "admin/reference-genomes", "Reference Data with Data Managers", "Galaxy Server administration", "/topics/admin/tutorials/reference-genomes/tutorial.html" ] ] }, "melpetera/idchoice/idchoice": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/melpetera/idchoice/idchoice/19.12", "19.12" ] ], "tutorials": [ [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "lecorguille/xcms_summary/abims_xcms_summary": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/abims_xcms_summary/3.12.0+galaxy0", "3.12.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/lcms-preprocessing", "Mass spectrometry: LC-MS preprocessing with XCMS", "Metabolomics", "/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html" ] ] }, "richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0", "0.5.0+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/ncbi-fcs", "Screening assembled genomes for contamination using NCBI FCS", "Sequence analysis", "/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html" ] ] }, "iuc/ncbi_fcs_gx/ncbi_fcs_gx": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0", "0.5.0+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/ncbi-fcs", "Screening assembled genomes for contamination using NCBI FCS", "Sequence analysis", "/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html" ] ] }, "iuc/varvamp/varvamp": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/varvamp/varvamp/1.2.2+galaxy0", "1.2.2+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/viral_primer_design", "Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes", "Sequence analysis", "/topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html" ] ] }, "devteam/ncbi_blast_plus/ncbi_makeblastdb": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/2.14.1+galaxy2", "2.14.1+galaxy2" ] ], "tutorials": [ [ "sequence-analysis/viral_primer_design", "Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes", "Sequence analysis", "/topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html" ] ] }, "devteam/emboss_5/EMBOSS: degapseq20": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: degapseq20/5.0.0", "5.0.0" ] ], "tutorials": [ [ "sequence-analysis/viral_primer_design", "Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes", "Sequence analysis", "/topics/sequence-analysis/tutorials/viral_primer_design/tutorial.html" ] ] }, "iuc/trimal/trimal": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trimal/trimal/1.5.0+galaxy1", "1.5.0+galaxy1" ] ], "tutorials": [ [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ] ] }, "iuc/quicktree/quicktree": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/quicktree/quicktree/2.5+galaxy0", "2.5+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ] ] }, "iuc/ete_treeviewer/ete_treeviewer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ete_treeviewer/ete_treeviewer/3.1.3+galaxy0", "3.1.3+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ] ] }, "bgruening/tapscan/tapscan_classify": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/tapscan/tapscan_classify/4.76+galaxy0", "4.76+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/tapscan-streptophyte-algae", "Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants", "Sequence analysis", "/topics/sequence-analysis/tutorials/tapscan-streptophyte-algae/tutorial.html" ] ] }, "iuc/pycoqc/pycoqc": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pycoqc/pycoqc/2.5.2+galaxy0", "2.5.2+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/quality-control", "Quality Control", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-control/tutorial.html" ] ] }, "iuc/fastqe/fastqe": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fastqe/fastqe/0.3.1+galaxy0", "0.3.1+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/quality-control", "Quality Control", "Sequence analysis", "/topics/sequence-analysis/tutorials/quality-control/tutorial.html" ] ] }, "iuc/seqtk/seqtk_trimfq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1", "1.3.1" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "iuc/seqtk/seqtk_mergepe": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1", "1.3.1" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "iuc/qiime_align_seqs/qiime_align_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0", "1.9.1.0" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "iuc/mothur_degap_seqs/mothur_degap_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "ecology/aligned_to_consensus/aligned_to_consensus": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0", "1.0.0" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "devteam/fastx_reverse_complement/cshl_fastx_reverse_complement": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0", "1.0.2+galaxy0" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "devteam/fastq_masker_by_quality/fastq_masker_by_quality": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.1.5", "1.1.5" ] ], "tutorials": [ [ "sequence-analysis/Manage_AB1_Sanger", "Clean and manage Sanger sequences from raw files to aligned consensus", "Sequence analysis", "/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html" ] ] }, "iuc/ena_upload/ena_upload": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.7.1", "0.7.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.2", "0.3.2" ] ], "tutorials": [ [ "galaxy-interface/upload-data-to-ena", "Submitting sequence data to ENA", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html" ] ] }, "ieguinoa/ena_webin_cli/ena_consensus_submit": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_consensus_submit/4.3.0", "4.3.0" ] ], "tutorials": [ [ "galaxy-interface/upload-data-to-ena", "Submitting sequence data to ENA", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.html" ] ] }, "iuc/intermine_galaxy_exchange/galaxy_intermine_exchange": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1", "0.0.1" ] ], "tutorials": [ [ "galaxy-interface/intermine", "InterMine integration with Galaxy", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/intermine/tutorial.html" ] ] }, "intermine": { "tool_id": [ [ "intermine", "intermine" ] ], "tutorials": [ [ "galaxy-interface/intermine", "InterMine integration with Galaxy", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/intermine/tutorial.html" ] ] }, "bgruening/text_processing/tp_tac": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0", "1.1.0" ] ], "tutorials": [ [ "galaxy-interface/workflow-editor", "Creating, Editing and Importing Galaxy Workflows", "Using Galaxy and Managing your Data", "/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html" ] ] }, "kellrott/regex_replace/regex_replace": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0", "1.0.0" ] ], "tutorials": [ [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ] ] }, "iuc/stacks_refmap/stacks_refmap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0", "1.46.0" ] ], "tutorials": [ [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ] ] }, "devteam/bwa_wrappers/bwa_wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", "1.2.3" ] ], "tutorials": [ [ "ecology/ref-based-rad-seq", "RAD-Seq Reference-based data analysis", "Ecology", "/topics/ecology/tutorials/ref-based-rad-seq/tutorial.html" ] ] }, "ecology/phylogenetic_occupancy_matcher/phylogenetic_occupancy_matcher": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/phylogenetic_occupancy_matcher/phylogenetic_occupancy_matcher/1.0+galaxy0", "1.0+galaxy0" ] ], "tutorials": [ [ "ecology/phylodiversity_workflow", "Phylodiversity analysis quick tutorial", "Ecology", "/topics/ecology/tutorials/phylodiversity_workflow/tutorial.html" ] ] }, "ecology/phylo_index/phylo_index": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/phylo_index/phylo_index/1.0+galaxy0", "1.0+galaxy0" ] ], "tutorials": [ [ "ecology/phylodiversity_workflow", "Phylodiversity analysis quick tutorial", "Ecology", "/topics/ecology/tutorials/phylodiversity_workflow/tutorial.html" ] ] }, "ecology/estimate_endem/estimate_endem": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/estimate_endem/estimate_endem/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "ecology/phylodiversity_workflow", "Phylodiversity analysis quick tutorial", "Ecology", "/topics/ecology/tutorials/phylodiversity_workflow/tutorial.html" ] ] }, "ecology/crsconverter/crsconverter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/crsconverter/crsconverter/1.1+galaxy0", "1.1+galaxy0" ] ], "tutorials": [ [ "ecology/phylodiversity_workflow", "Phylodiversity analysis quick tutorial", "Ecology", "/topics/ecology/tutorials/phylodiversity_workflow/tutorial.html" ] ] }, "bgruening/yolo_predict/yolo_predict": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/yolo_predict/yolo_predict/8.3.0+galaxy5", "8.3.0+galaxy5" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/yolo_predict/yolo_predict/8.3.0+galaxy2", "8.3.0+galaxy2" ] ], "tutorials": [ [ "ecology/yolo_predict_deepsea", "Object detection with YOLO", "Ecology", "/topics/ecology/tutorials/yolo_predict_deepsea/tutorial.html" ] ] }, "ecology/pampa_presabs/pampa_presabs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2", "0.0.2" ] ], "tutorials": [ [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ] ] }, "ecology/pampa_plotglm/pampa_plotglm": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2", "0.0.2" ] ], "tutorials": [ [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ] ] }, "ecology/pampa_glmsp/pampa_glmsp": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2", "0.0.2" ] ], "tutorials": [ [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ] ] }, "ecology/pampa_glmcomm/pampa_glmcomm": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/0.0.2", "0.0.2" ] ], "tutorials": [ [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ] ] }, "ecology/pampa_communitymetrics/pampa_communitymetrics": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/0.0.2", "0.0.2" ] ], "tutorials": [ [ "ecology/PAMPA-toolsuite-tutorial", "Compute and analyze biodiversity metrics with PAMPA toolsuite", "Ecology", "/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html" ] ] }, "ecology/tool_anonymization/tool_anonymization": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ] ] }, "ecology/ecology_stat_presence_abs/ecology_stat_presence_abs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ] ] }, "ecology/ecology_presence_abs_abund/ecology_presence_abs_abund": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ] ] }, "ecology/ecology_link_between_var/ecology_link_between_var": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ] ] }, "ecology/ecology_homogeneity_normality/ecology_homogeneity_normality": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ] ] }, "ecology/ecology_beta_diversity/ecology_beta_diversity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/biodiversity-data-exploration", "Biodiversity data exploration", "Ecology", "/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html" ] ] }, "iuc/obi_uniq/obi_uniq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "iuc/obi_tab/obi_tab": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "iuc/obi_stat/obi_stat": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "iuc/obi_ngsfilter/obi_ngsfilter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "iuc/obi_illumina_pairend/obi_illumina_pairend": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "iuc/obi_grep/obi_grep": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "iuc/obi_clean/obi_clean": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "iuc/obi_annotate/obi_annotate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13", "1.2.13" ] ], "tutorials": [ [ "ecology/Obitools-metabarcoding", "Metabarcoding/eDNA through Obitools", "Ecology", "/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html" ] ] }, "interactive_tool_metashark": { "tool_id": [ [ "interactive_tool_metashark", "interactive_tool_metashark" ] ], "tutorials": [ [ "ecology/MetaShARK_tutorial", "Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities", "Ecology", "/topics/ecology/tutorials/MetaShARK_tutorial/tutorial.html" ] ] }, "ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ] ] }, "ecology/ecoregion_clara_cluster/ecoregion_clara_cluster": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/ecoregion_clara_cluster/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "ecology/Ecoregionalization_tutorial", "Ecoregionalization workflow tutorial", "Ecology", "/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html" ] ] }, "mnhn65mo/tabular_to_csv/tab2csv_R": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/mnhn65mo/tabular_to_csv/tab2csv_R/0.1", "0.1" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "mnhn65mo/regionalgam/flight-curve": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/mnhn65mo/regionalgam/flight-curve/1.0.0", "1.0.0" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "mnhn65mo/csv_to_tabular/csv2tab_R": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/mnhn65mo/csv_to_tabular/csv2tab_R/0.1", "0.1" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "ecology/regionalgam_plot_trend/regionalgam_plot_trend": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/regionalgam_plot_trend/regionalgam_plot_trend/1.5", "1.5" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "ecology/regionalgam_gls/regionalgam_gls": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/regionalgam_gls/regionalgam_gls/1.5", "1.5" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "ecology/regionalgam_glmmpql/regionalgam_glmmpql": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/regionalgam_glmmpql/regionalgam_glmmpql/1.5", "1.5" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "ecology/regionalgam_flight_curve/regionalgam_flight_curve": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/regionalgam_flight_curve/regionalgam_flight_curve/1.5", "1.5" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "ecology/regionalgam_autocor_acf/regionalgam_autocor_acf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/regionalgam_autocor_acf/regionalgam_autocor_acf/1.5", "1.5" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "ecology/regionalgam_ab_index/regionalgam_ab_index": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/regionalgam_ab_index/regionalgam_ab_index/1.5", "1.5" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "mergeCols1": { "tool_id": [ [ "mergeCols1", "mergeCols1" ] ], "tutorials": [ [ "ecology/regionalGAM", "Regional GAM", "Ecology", "/topics/ecology/tutorials/regionalGAM/tutorial.html" ] ] }, "ecology/srs_spectral_indices/srs_spectral_indices": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1", "0.0.1" ] ], "tutorials": [ [ "ecology/remote-sensing", "Sentinel 2 biodiversity", "Ecology", "/topics/ecology/tutorials/remote-sensing/tutorial.html" ] ] }, "ecology/srs_process_data/srs_process_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/srs_process_data/srs_process_data/0.0.1", "0.0.1" ] ], "tutorials": [ [ "ecology/remote-sensing", "Sentinel 2 biodiversity", "Ecology", "/topics/ecology/tutorials/remote-sensing/tutorial.html" ] ] }, "ecology/srs_preprocess_s2/srs_preprocess_s2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1", "0.0.1" ] ], "tutorials": [ [ "ecology/remote-sensing", "Sentinel 2 biodiversity", "Ecology", "/topics/ecology/tutorials/remote-sensing/tutorial.html" ] ] }, "ecology/srs_pca/srs_pca": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/srs_pca/srs_pca/0.0.1", "0.0.1" ] ], "tutorials": [ [ "ecology/remote-sensing", "Sentinel 2 biodiversity", "Ecology", "/topics/ecology/tutorials/remote-sensing/tutorial.html" ] ] }, "ecology/srs_global_indices/srs_global_indices": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1", "0.0.1" ] ], "tutorials": [ [ "ecology/remote-sensing", "Sentinel 2 biodiversity", "Ecology", "/topics/ecology/tutorials/remote-sensing/tutorial.html" ] ] }, "ecology/srs_diversity_maps/srs_diversity_maps": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1", "0.0.1" ] ], "tutorials": [ [ "ecology/remote-sensing", "Sentinel 2 biodiversity", "Ecology", "/topics/ecology/tutorials/remote-sensing/tutorial.html" ] ] }, "iuc/stacks_genotypes/stacks_genotypes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/stacks_genotypes/stacks_genotypes/1.46.0", "1.46.0" ] ], "tutorials": [ [ "ecology/genetic-map-rad-seq", "RAD-Seq to construct genetic maps", "Ecology", "/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html" ] ] }, "padge/phykit/phykit_alignment_based": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0", "0.1.0" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ] ] }, "padge/clipkit/clipkit": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0", "0.1.0" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ] ] }, "iuc/proteinortho_grab_proteins/proteinortho_grab_proteins": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1", "6.0.14+galaxy2.9.1" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ] ] }, "iuc/proteinortho/proteinortho": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1", "6.0.14+galaxy2.9.1" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ] ] }, "bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02", "3.02" ] ], "tutorials": [ [ "ecology/phylogeny-data-prep", "Preparing genomic data for phylogeny reconstruction", "Ecology", "/topics/ecology/tutorials/phylogeny-data-prep/tutorial.html" ] ] }, "iuc/prodigal/prodigal": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0", "2.6.3+galaxy0" ] ], "tutorials": [ [ "ecology/marine_omics_bgc", "Marine Omics identifying biosynthetic gene clusters", "Ecology", "/topics/ecology/tutorials/marine_omics_bgc/tutorial.html" ] ] }, "ecology/sanntis_marine/sanntis_marine": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1", "0.9.3.5+galaxy1" ] ], "tutorials": [ [ "ecology/marine_omics_bgc", "Marine Omics identifying biosynthetic gene clusters", "Ecology", "/topics/ecology/tutorials/marine_omics_bgc/tutorial.html" ] ] }, "ecology/SanntiS_marine/SanntiS_marine": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/SanntiS_marine/SanntiS_marine/0.9.3.5+galaxy1", "0.9.3.5+galaxy1" ] ], "tutorials": [ [ "ecology/marine_omics_bgc", "Marine Omics identifying biosynthetic gene clusters", "Ecology", "/topics/ecology/tutorials/marine_omics_bgc/tutorial.html" ] ] }, "climate/cdo_operations/cdo_operations": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0", "2.0.0+galaxy0" ] ], "tutorials": [ [ "ecology/x-array-map-plot", "Visualization of Climate Data using NetCDF xarray Map Plotting", "Ecology", "/topics/ecology/tutorials/x-array-map-plot/tutorial.html" ] ] }, "ecology/gdal_ogr2ogr/gdal_ogr2ogr": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/gdal_ogr2ogr/gdal_ogr2ogr/3.0.0", "3.0.0" ] ], "tutorials": [ [ "ecology/gbif_cleaning", "Cleaning GBIF data for the use in Ecology", "Ecology", "/topics/ecology/tutorials/gbif_cleaning/tutorial.html" ] ] }, "ecology/cb_ivr/cb_ivr": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/cb_ivr/cb_ivr/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/champs-blocs", "Champs blocs indicators", "Ecology", "/topics/ecology/tutorials/champs-blocs/tutorial.html" ] ] }, "ecology/cb_div/cb_div": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/cb_div/cb_div/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/champs-blocs", "Champs blocs indicators", "Ecology", "/topics/ecology/tutorials/champs-blocs/tutorial.html" ] ] }, "ecology/cb_dissim/cb_dissim": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/cb_dissim/cb_dissim/0.0.0", "0.0.0" ] ], "tutorials": [ [ "ecology/champs-blocs", "Champs blocs indicators", "Ecology", "/topics/ecology/tutorials/champs-blocs/tutorial.html" ] ] }, "cb_qecb": { "tool_id": [ [ "cb_qecb", "cb_qecb" ] ], "tutorials": [ [ "ecology/champs-blocs", "Champs blocs indicators", "Ecology", "/topics/ecology/tutorials/champs-blocs/tutorial.html" ] ] }, "cb_ivr": { "tool_id": [ [ "cb_ivr", "cb_ivr" ] ], "tutorials": [ [ "ecology/champs-blocs", "Champs blocs indicators", "Ecology", "/topics/ecology/tutorials/champs-blocs/tutorial.html" ] ] }, "cb_eco": { "tool_id": [ [ "cb_eco", "cb_eco" ] ], "tutorials": [ [ "ecology/champs-blocs", "Champs blocs indicators", "Ecology", "/topics/ecology/tutorials/champs-blocs/tutorial.html" ] ] }, "ecology/obisindicators/obisindicators": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.2", "0.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.1", "0.0.1" ] ], "tutorials": [ [ "ecology/obisindicators", "Obis marine indicators", "Ecology", "/topics/ecology/tutorials/obisindicators/tutorial.html" ] ] }, "interactive_tool_metashrimps": { "tool_id": [ [ "interactive_tool_metashrimps", "interactive_tool_metashrimps" ] ], "tutorials": [ [ "ecology/Metashrimps_tutorial", "Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS", "Ecology", "/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html" ] ] }, "interactive_tool_wallace": { "tool_id": [ [ "interactive_tool_wallace", "interactive_tool_wallace" ] ], "tutorials": [ [ "ecology/species-distribution-modeling", "Species distribution modeling", "Ecology", "/topics/ecology/tutorials/species-distribution-modeling/tutorial.html" ] ] }, "interactive_tool_holoviz": { "tool_id": [ [ "interactive_tool_holoviz", "interactive_tool_holoviz" ] ], "tutorials": [ [ "ecology/ndvi_openeo", "From NDVI data with OpenEO to time series visualisation with Holoviews", "Ecology", "/topics/ecology/tutorials/ndvi_openeo/tutorial.html" ] ] }, "ecology/wormsmeasurements/WormsMeasurements": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/wormsmeasurements/WormsMeasurements/0.1.1", "0.1.1" ] ], "tutorials": [ [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ] ] }, "ecology/claraguess/ClaraGuess": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/claraguess/ClaraGuess/0.1.2", "0.1.2" ] ], "tutorials": [ [ "ecology/ecoregiolifetraits", "Life Traits Ecoregionalization workflow", "Ecology", "/topics/ecology/tutorials/ecoregiolifetraits/tutorial.html" ] ] }, "rnateam/cmsearch_deoverlap/cmsearch_deoverlap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy2", "0.08+galaxy2" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/seqprep/seqprep": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seqprep/seqprep/1.3.2+galaxy0", "1.3.2+galaxy0" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/prinseq/prinseq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4+galaxy2", "0.20.4+galaxy2" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/mapseq/mapseq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0", "2.1.1+galaxy0" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/fastq_dl/fastq_dl": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fastq_dl/fastq_dl/3.0.1+galaxy0", "3.0.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/fastq_dl/fastq_dl/3.0.0+galaxy0", "3.0.0+galaxy0" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/biom_convert/biom_convert": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1", "2.1.15+galaxy1" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/ampvis2_load/ampvis2_load": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0", "2.8.9+galaxy0" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/ampvis2_heatmap/ampvis2_heatmap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_heatmap/ampvis2_heatmap/2.8.9+galaxy1", "2.8.9+galaxy1" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "devteam/fasta_formatter/cshl_fasta_formatter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2", "1.0.1+galaxy2" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "devteam/concat/gops_concat_1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1", "1.0.1" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "bgruening/mgnify_seqprep/mgnify_seqprep": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/mgnify_seqprep/mgnify_seqprep/1.2+galaxy0", "1.2+galaxy0" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "bgruening/infernal/infernal_cmsearch": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.5+galaxy0", "1.1.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0", "1.1.4+galaxy0" ] ], "tutorials": [ [ "microbiome/mgnify-amplicon", "MGnify v5.0 Amplicon Pipeline", "Microbiome", "/topics/microbiome/tutorials/mgnify-amplicon/tutorial.html" ] ] }, "iuc/phyloseq_from_dada2/phyloseq_from_dada2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.50.0+galaxy3", "1.50.0+galaxy3" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_seqcounts/dada2_seqCounts": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_plotqualityprofile/dada2_plotQualityProfile": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_mergepairs/dada2_mergePairs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_makesequencetable/dada2_makeSequenceTable": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_learnerrors/dada2_learnErrors": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_filterandtrim/dada2_filterAndTrim": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_dada/dada2_dada": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "interactive_tool_phyloseq": { "tool_id": [ [ "interactive_tool_phyloseq", "interactive_tool_phyloseq" ] ], "tutorials": [ [ "microbiome/dada-16S", "Building an amplicon sequence variant (ASV) table from 16S data using DADA2", "Microbiome", "/topics/microbiome/tutorials/dada-16S/tutorial.html" ] ] }, "iuc/samtools_depth/samtools_depth": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy2", "1.15.1+galaxy2" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/samtools_coverage/samtools_coverage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2", "1.15.1+galaxy2" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/mlst/mlst": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst/2.22.0", "2.22.0" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1", "1.2+galaxy1" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/ggplot2_heatmap/ggplot2_heatmap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0", "3.4.0+galaxy0" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/clair3/clair3": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/0.1.12+galaxy0", "0.1.12+galaxy0" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/bamtools_split_mapped/bamtools_split_mapped": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2", "2.5.2+galaxy2" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/abricate/abricate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1", "1.0.1" ] ], "tutorials": [ [ "microbiome/pathogen-detection-from-nanopore-foodborne-data", "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition", "Microbiome", "/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html" ] ] }, "iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0", "1.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ] ] }, "iuc/mothur_seq_error/mothur_seq_error": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ] ] }, "iuc/mothur_make_contigs/mothur_make_contigs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ] ] }, "iuc/mothur_get_groups/mothur_get_groups": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0", "1.39.5.0" ] ], "tutorials": [ [ "microbiome/mothur-miseq-sop", "16S Microbial Analysis with mothur (extended)", "Microbiome", "/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html" ] ] }, "iuc/plasflow/PlasFlow": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0", "1.0" ] ], "tutorials": [ [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "iuc/miniasm/miniasm": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0", "0.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0", "0.2+galaxy0" ] ], "tutorials": [ [ "microbiome/plasmid-metagenomics-nanopore", "Antibiotic resistance detection", "Microbiome", "/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html" ] ] }, "bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0", "0.2.0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics-short", "Metatranscriptomics analysis using microbiome RNA-seq data (short)", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html" ] ] }, "mbernt/maxbin2/maxbin2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6", "2.2.7+galaxy6" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/semibin/semibin": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.1.0+galaxy1", "2.1.0+galaxy1" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0", "2.17+galaxy0" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/metabat2/metabat2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0", "2.17+galaxy0" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1", "1.1.7+galaxy1" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/das_tool/das_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/das_tool/das_tool/1.1.7+galaxy1", "1.1.7+galaxy1" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2", "1.1.0+galaxy2" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2", "1.1.0+galaxy2" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/concoct_cut_up_fasta/concoct_cut_up_fasta": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2", "1.1.0+galaxy2" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/concoct_coverage_table/concoct_coverage_table": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2", "1.1.0+galaxy2" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/concoct/concoct": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2", "1.1.0+galaxy2" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "iuc/binette/binette": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.2.0+galaxy0", "1.2.0+galaxy0" ] ], "tutorials": [ [ "microbiome/metagenomics-binning", "Binning of metagenomic sequencing data", "Microbiome", "/topics/microbiome/tutorials/metagenomics-binning/tutorial.html" ] ] }, "bebatut/combine_metaphlan2_humann2/combine_metaphlan_humann": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan_humann/0.3.0", "0.3.0" ] ], "tutorials": [ [ "microbiome/metatranscriptomics", "Metatranscriptomics analysis using microbiome RNA-seq data", "Microbiome", "/topics/microbiome/tutorials/metatranscriptomics/tutorial.html" ] ] }, "iuc/krakentools_beta_diversity/krakentools_beta_diversity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1", "1.2+galaxy1" ] ], "tutorials": [ [ "microbiome/diversity", "Calculating α and β diversity from microbiome taxonomic data", "Microbiome", "/topics/microbiome/tutorials/diversity/tutorial.html" ] ] }, "iuc/krakentools_alpha_diversity/krakentools_alpha_diversity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1", "1.2+galaxy1" ] ], "tutorials": [ [ "microbiome/diversity", "Calculating α and β diversity from microbiome taxonomic data", "Microbiome", "/topics/microbiome/tutorials/diversity/tutorial.html" ] ] }, "iuc/kraken_biom/kraken_biom": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1", "1.2.0+galaxy1" ] ], "tutorials": [ [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ] ] }, "interactive_tool_phinch": { "tool_id": [ [ "interactive_tool_phinch", "interactive_tool_phinch" ] ], "tutorials": [ [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ] ] }, "interactive_tool_pavian": { "tool_id": [ [ "interactive_tool_pavian", "interactive_tool_pavian" ] ], "tutorials": [ [ "microbiome/taxonomic-profiling", "Taxonomic Profiling and Visualization of Metagenomic Data", "Microbiome", "/topics/microbiome/tutorials/taxonomic-profiling/tutorial.html" ] ] }, "iuc/datamash_reverse/datamash_reverse": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0", "1.1.0" ] ], "tutorials": [ [ "microbiome/nanopore-16S-metagenomics", "16S Microbial analysis with Nanopore data", "Microbiome", "/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html" ] ] }, "estrain/add_column_headers/add_column_headers": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/estrain/add_column_headers/add_column_headers/0.1.3", "0.1.3" ] ], "tutorials": [ [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ] ] }, "devteam/count_gff_features/count_gff_features": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.2", "0.2" ] ], "tutorials": [ [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ] ] }, "CONVERTER_fasta_to_tabular": { "tool_id": [ [ "CONVERTER_fasta_to_tabular", "CONVERTER_fasta_to_tabular" ] ], "tutorials": [ [ "microbiome/metaplasmidome_query", "Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data", "Microbiome", "/topics/microbiome/tutorials/metaplasmidome_query/tutorial.html" ] ] }, "bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0", "3.3.2.0.0" ] ], "tutorials": [ [ "epigenetics/tal1-binding-site-identification", "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)", "Epigenetics", "/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html" ] ] }, "rnateam/metilene/metilene": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1", "0.2.6.1" ] ], "tutorials": [ [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ] ] }, "iuc/bwameth/bwameth": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.7+galaxy0", "0.2.7+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3", "0.2.0.3" ] ], "tutorials": [ [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ] ] }, "bgruening/pileometh/pileometh": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.5.2+galaxy0", "0.5.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0", "0.3.0" ] ], "tutorials": [ [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ] ] }, "bgruening/deeptools_plot_profile/deeptools_plot_profile": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.5.4+galaxy0", "3.5.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0", "2.5.1.1.0" ] ], "tutorials": [ [ "epigenetics/methylation-seq", "DNA Methylation data analysis", "Epigenetics", "/topics/epigenetics/tutorials/methylation-seq/tutorial.html" ] ] }, "iuc/idr/idr": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/idr/idr/2.0.3", "2.0.3" ] ], "tutorials": [ [ "epigenetics/cut_and_run", "CUT&RUN data analysis", "Epigenetics", "/topics/epigenetics/tutorials/cut_and_run/tutorial.html" ] ] }, "kpbioteam/ewastools/minfi_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0", "2.1.0" ] ], "tutorials": [ [ "epigenetics/ewas-suite", "Infinium Human Methylation BeadChip", "Epigenetics", "/topics/epigenetics/tutorials/ewas-suite/tutorial.html" ] ] }, "kpbioteam/clusterprofiler_go/clusterprofiler_go": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0", "0.1.0" ] ], "tutorials": [ [ "epigenetics/ewas-suite", "Infinium Human Methylation BeadChip", "Epigenetics", "/topics/epigenetics/tutorials/ewas-suite/tutorial.html" ] ] }, "kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0", "0.1.0" ] ], "tutorials": [ [ "epigenetics/ewas-suite", "Infinium Human Methylation BeadChip", "Epigenetics", "/topics/epigenetics/tutorials/ewas-suite/tutorial.html" ] ] }, "kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0", "0.1.0" ] ], "tutorials": [ [ "epigenetics/ewas-suite", "Infinium Human Methylation BeadChip", "Epigenetics", "/topics/epigenetics/tutorials/ewas-suite/tutorial.html" ] ] }, "bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.7.6+galaxy1", "3.7.6+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/3.4.3.0", "3.4.3.0" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hicpca/hicexplorer_hicpca": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/3.7.6+galaxy1", "3.7.6+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/3.6+galaxy1", "3.6+galaxy1" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/3.7.6+galaxy1", "3.7.6+galaxy1" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hicinfo/hicexplorer_hicinfo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicinfo/hicexplorer_hicinfo/3.7.6+galaxy1", "3.7.6+galaxy1" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/3.7.6+galaxy1", "3.7.6+galaxy1" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hicfindrestrictionsites/hicexplorer_hicfindrestrictionsites": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindrestrictionsites/hicexplorer_hicfindrestrictionsites/3.7.6+galaxy1", "3.7.6+galaxy1" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hicdetectloops/hicexplorer_hicdetectloops": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicdetectloops/hicexplorer_hicdetectloops/3.7.6+galaxy1", "3.7.6+galaxy1" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.7.6+galaxy1", "3.7.6+galaxy1" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/3.7.6+galaxy1", "3.7.6+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/3.4.3.0", "3.4.3.0" ] ], "tutorials": [ [ "epigenetics/hicexplorer", "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer", "Epigenetics", "/topics/epigenetics/tutorials/hicexplorer/tutorial.html" ] ] }, "ecology/timeseries_extraction/timeseries_extraction": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0", "2022.3.0+galaxy0" ] ], "tutorials": [ [ "climate/argo_pangeo", "Analyse Argo data", "Earth Data science", "/topics/climate/tutorials/argo_pangeo/tutorial.html" ] ] }, "ecology/tool_odv_history/tool_odv_history": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/tool_odv_history/tool_odv_history/1.2+galaxy2", "1.2+galaxy2" ] ], "tutorials": [ [ "climate/ocean_qcv_analysis", "Nitrate DMQC for autonomous platforms such as Argo floats", "Earth Data science", "/topics/climate/tutorials/ocean_qcv_analysis/tutorial.html" ] ] }, "ecology/tool_odv/tool_odv": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/tool_odv/tool_odv/1.3+galaxy2", "1.3+galaxy2" ] ], "tutorials": [ [ "climate/ocean_qcv_analysis", "Nitrate DMQC for autonomous platforms such as Argo floats", "Earth Data science", "/topics/climate/tutorials/ocean_qcv_analysis/tutorial.html" ] ] }, "ecology/tool_biogeochemical_calibration/tool_biogeochemical_calibration": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/tool_biogeochemical_calibration/tool_biogeochemical_calibration/2.1+galaxy2", "2.1+galaxy2" ] ], "tutorials": [ [ "climate/ocean_qcv_analysis", "Nitrate DMQC for autonomous platforms such as Argo floats", "Earth Data science", "/topics/climate/tutorials/ocean_qcv_analysis/tutorial.html" ] ] }, "ecology/harmonize_insitu_to_netcdf/harmonize_insitu_to_netcdf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/harmonize_insitu_to_netcdf/harmonize_insitu_to_netcdf/3.0+galaxy1", "3.0+galaxy1" ] ], "tutorials": [ [ "climate/ocean_qcv_analysis", "Nitrate DMQC for autonomous platforms such as Argo floats", "Earth Data science", "/topics/climate/tutorials/ocean_qcv_analysis/tutorial.html" ] ] }, "climate/psy_maps/psy_maps": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/climate/psy_maps/psy_maps/1.2.1", "1.2.1" ] ], "tutorials": [ [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ] ] }, "climate/cds_essential_variability/cds_essential_variability": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/climate/cds_essential_variability/cds_essential_variability/0.1.4", "0.1.4" ] ], "tutorials": [ [ "climate/climate-101", "Getting your hands-on climate data", "Earth Data science", "/topics/climate/tutorials/climate-101/tutorial.html" ] ] }, "ecology/divand_full_analysis/divand_full_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0", "0.1.0+galaxy0" ] ], "tutorials": [ [ "climate/ocean-variables", "Ocean's variables study", "Earth Data science", "/topics/climate/tutorials/ocean-variables/tutorial.html" ] ] }, "interactive_tool_divand": { "tool_id": [ [ "interactive_tool_divand", "interactive_tool_divand" ] ], "tutorials": [ [ "climate/ocean-variables", "Ocean's variables study", "Earth Data science", "/topics/climate/tutorials/ocean-variables/tutorial.html" ] ] }, "climate/ctsm_fates/ctsm_fates": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1", "2.0.1" ] ], "tutorials": [ [ "climate/fates", "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)", "Earth Data science", "/topics/climate/tutorials/fates/tutorial.html" ] ] }, "ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0", "0.18.2+galaxy0" ] ], "tutorials": [ [ "climate/pangeo", "Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools", "Earth Data science", "/topics/climate/tutorials/pangeo/tutorial.html" ] ] }, "interactive_tool_pangeo_notebook": { "tool_id": [ [ "interactive_tool_pangeo_notebook", "interactive_tool_pangeo_notebook" ] ], "tutorials": [ [ "climate/pangeo-notebook", "Pangeo Notebook in Galaxy - Introduction to Xarray", "Earth Data science", "/topics/climate/tutorials/pangeo-notebook/tutorial.html" ] ] }, "muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1", "0.3.0+galaxy1" ] ], "tutorials": [ [ "materials-science/muon-stopping-sites-muairss-uep", "Finding the muon stopping site with pymuon-suite in Galaxy", "Materials Science", "/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html" ] ] }, "muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read/0.3.0+galaxy0", "0.3.0+galaxy0" ] ], "tutorials": [ [ "materials-science/muon-stopping-sites-muairss-uep", "Finding the muon stopping site with pymuon-suite in Galaxy", "Materials Science", "/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html" ] ] }, "setup": { "tool_id": [ [ "setup", "setup" ] ], "tutorials": [ [ "computational-chemistry/md-simulation-namd", "Running molecular dynamics simulations using NAMD", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html" ] ] }, "namd_nvt": { "tool_id": [ [ "namd_nvt", "namd_nvt" ] ], "tutorials": [ [ "computational-chemistry/md-simulation-namd", "Running molecular dynamics simulations using NAMD", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html" ] ] }, "namd_npt": { "tool_id": [ [ "namd_npt", "namd_npt" ] ], "tutorials": [ [ "computational-chemistry/md-simulation-namd", "Running molecular dynamics simulations using NAMD", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html" ] ] }, "minimizer": { "tool_id": [ [ "minimizer", "minimizer" ] ], "tutorials": [ [ "computational-chemistry/md-simulation-namd", "Running molecular dynamics simulations using NAMD", "Computational chemistry", "/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html" ] ] }, "chemteam/vmd_hbonds/vmd_hbonds": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/vmd_hbonds/vmd_hbonds/1.9.3", "1.9.3" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "chemteam/gmx_merge_topology_files/gmx_merge_topology_files": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0+galaxy0", "3.2.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0", "3.2.0" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "chemteam/gmx_energy/gmx_energy": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_energy/gmx_energy/2020.4+galaxy0", "2020.4+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "chemteam/bio3d_pca_visualize/bio3d_pca_visualize": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca_visualize/bio3d_pca_visualize/2.3.4", "2.3.4" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "chemteam/ambertools_acpype/ambertools_acpype": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/21.3+galaxy0", "21.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11", "19.11" ] ], "tutorials": [ [ "computational-chemistry/htmd-analysis", "High Throughput Molecular Dynamics and Analysis", "Computational chemistry", "/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html" ] ] }, "bgruening/rdconf/rdconf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0", "2020.03.4+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/zauberkugel", "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib", "Computational chemistry", "/topics/computational-chemistry/tutorials/zauberkugel/tutorial.html" ] ] }, "bgruening/openbabel_addh/openbabel_addh": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1", "3.1.1+galaxy1" ] ], "tutorials": [ [ "computational-chemistry/zauberkugel", "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib", "Computational chemistry", "/topics/computational-chemistry/tutorials/zauberkugel/tutorial.html" ] ] }, "bgruening/align_it/ctb_alignit": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0", "1.0.4+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/zauberkugel", "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib", "Computational chemistry", "/topics/computational-chemistry/tutorials/zauberkugel/tutorial.html" ] ] }, "bgruening/sdf_to_tab/sdf_to_tab": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/2020.03.4+galaxy0", "2020.03.4+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/openbabel/ctb_remIons": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0", "1.0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/openbabel/ctb_remDuplicates": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0", "1.0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/openbabel/ctb_obgrep": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1", "0.1" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/openbabel/ctb_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_filter/1.0", "1.0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/openbabel/ctb_compound_convert": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1", "0.1" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/openbabel/ctb_change_title": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1", "0.0.1" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/fpocket/fpocket": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/fpocket/fpocket/3.1.4.2+galaxy0", "3.1.4.2+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/chemical_data_sources/ctb_online_data_fetch": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2", "0.2" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/chemfp/ctb_chemfp_nxn_clustering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1", "1.5.1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.4", "0.4" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/chemfp/ctb_chemfp_butina_clustering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5", "1.5" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/autodock_vina_prepare_receptor/prepare_receptor": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/1.5.7+galaxy0", "1.5.7+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/autodock_vina_prepare_box/prepare_box": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.5+galaxy0", "2021.03.5+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.4+galaxy0", "2021.03.4+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "bgruening/autodock_vina/docking": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0", "1.2.3+galaxy0" ] ], "tutorials": [ [ "computational-chemistry/cheminformatics", "Protein-ligand docking", "Computational chemistry", "/topics/computational-chemistry/tutorials/cheminformatics/tutorial.html" ] ] }, "xchem_pose_scoring": { "tool_id": [ [ "xchem_pose_scoring", "xchem_pose_scoring" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/xchem_transfs_scoring/xchem_transfs_scoring": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/0.4.0", "0.4.0" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/sucos_max_score/sucos_max_score": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/2020.03.4+galaxy0", "2020.03.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3", "0.2.3" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/rxdock_rbdock/rxdock_rbdock": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/0.1.5", "0.1.5" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/rxdock_rbcavity/rxdock_rbcavity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/0.1.5", "0.1.5" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/rdock_rbdock/rdock_rbdock": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4", "0.1.4" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/rdock_rbcavity/rdock_rbcavity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1", "0.1" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/enumerate_charges/enumerate_charges": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0", "2020.03.4+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1", "0.1" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0", "2013.1-0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1", "0.1.1" ] ], "tutorials": [ [ "computational-chemistry/covid19-docking", "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring", "Computational chemistry", "/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html" ] ] }, "chemteam/mdanalysis_rdf/mdanalysis_rdf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf/0.19", "0.19" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ] ] }, "chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot/0.1.3", "0.1.3" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ] ] }, "chemteam/mdanalysis_distance/mdanalysis_distance": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_distance/mdanalysis_distance/0.19", "0.19" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ] ] }, "chemteam/mdanalysis_dihedral/mdanalysis_dihedral": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_dihedral/mdanalysis_dihedral/0.19", "0.19" ] ], "tutorials": [ [ "computational-chemistry/analysis-md-simulations", "Analysis of molecular dynamics simulations", "Computational chemistry", "/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html" ] ] }, "bgruening/imagemagick_image_montage/imagemagick_image_montage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1", "7.1.2-2+galaxy1" ] ], "tutorials": [ [ "introduction/galaxy-intro-rdm", "Introduction to Galaxy as an RDM platform", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html" ] ] }, "export_remote": { "tool_id": [ [ "export_remote", "export_remote" ] ], "tutorials": [ [ "introduction/galaxy-intro-rdm", "Introduction to Galaxy as an RDM platform", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html" ] ] }, "iuc/snpeff/snpEff_build_gb": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0", "5.2+galaxy0" ] ], "tutorials": [ [ "introduction/galaxy-intro-ngs-data-managment", "NGS data logistics", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html" ] ] }, "iuc/biapy/biapy": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/biapy/biapy/3.6.8+galaxy0", "3.6.8+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/biapy/biapy/3.6.5+galaxy0", "3.6.5+galaxy0" ] ], "tutorials": [ [ "imaging/biapy", "Execute a BiaPy workflow in Galaxy", "Imaging", "/topics/imaging/tutorials/biapy/tutorial.html" ] ] }, "bgruening/json2yolosegment/json2yolosegment": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/json2yolosegment/json2yolosegment/8.3.0+galaxy2", "8.3.0+galaxy2" ] ], "tutorials": [ [ "imaging/yolo-segmentation-training", "Training Custom YOLO Models for Segmentation of Bioimages", "Imaging", "/topics/imaging/tutorials/yolo-segmentation-training/tutorial.html" ] ] }, "bgruening/cp_track_objects/cp_track_objects": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_track_objects/cp_track_objects/3.1.9+galaxy0", "3.1.9+galaxy0" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ] ] }, "bgruening/cp_tile/cp_tile": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_tile/cp_tile/3.1.9+galaxy0", "3.1.9+galaxy0" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ] ] }, "bgruening/cp_color_to_gray/cp_color_to_gray": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_color_to_gray/cp_color_to_gray/3.1.9+galaxy0", "3.1.9+galaxy0" ] ], "tutorials": [ [ "imaging/object-tracking-using-cell-profiler", "Object tracking using CellProfiler", "Imaging", "/topics/imaging/tutorials/object-tracking-using-cell-profiler/tutorial.html" ] ] }, "watsocam/palom/palom": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/watsocam/palom/palom/2022.8.2+galaxy0", "2022.8.2+galaxy0" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "perssond/quantification/quantification": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.6.0+galaxy0", "1.6.0+galaxy0" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "perssond/coreograph/unet_coreograph": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1", "2.2.8+galaxy1" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "perssond/basic_illumination/basic_illumination": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.1.1+galaxy2", "1.1.1+galaxy2" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "perssond/ashlar/ashlar": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.18.0+galaxy1", "1.18.0+galaxy1" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/vitessce_spatial/vitessce_spatial": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/3.5.1+galaxy0", "3.5.1+galaxy0" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/squidpy_spatial/squidpy_spatial": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy_spatial/squidpy_spatial/1.5.0+galaxy2", "1.5.0+galaxy2" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/scimap_phenotyping/scimap_phenotyping": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/2.1.0+galaxy2", "2.1.0+galaxy2" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/2.1.0+galaxy2", "2.1.0+galaxy2" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/rename_tiff_channels/rename_tiff_channels": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.2+galaxy1", "0.0.2+galaxy1" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/mesmer/mesmer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy3", "0.12.3+galaxy3" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/gate_finder/gate_finder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/gate_finder/gate_finder/3.5.1+galaxy0", "3.5.1+galaxy0" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "goeckslab/celesta/celesta": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/celesta/celesta/0.0.0.9+galaxy3", "0.0.0.9+galaxy3" ] ], "tutorials": [ [ "imaging/multiplex-tissue-imaging-TMA", "End-to-End Tissue Microarray Image Analysis with Galaxy-ME", "Imaging", "/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html" ] ] }, "ufz/omero_roi_import/omero_roi_import": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ufz/omero_roi_import/omero_roi_import/5.18.0+galaxy5", "5.18.0+galaxy5" ] ], "tutorials": [ [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ] ] }, "ufz/omero_metadata_import/omero_metadata_import": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ufz/omero_metadata_import/omero_metadata_import/5.18.0+galaxy7", "5.18.0+galaxy7" ] ], "tutorials": [ [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ] ] }, "ufz/omero_import/omero_import": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ufz/omero_import/omero_import/5.18.0+galaxy6", "5.18.0+galaxy6" ] ], "tutorials": [ [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ] ] }, "ufz/omero_get_value/omero_get_value": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ufz/omero_get_value/omero_get_value/5.18.0+galaxy3", "5.18.0+galaxy3" ] ], "tutorials": [ [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ] ] }, "ufz/omero_get_id/omero_get_id": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ufz/omero_get_id/omero_get_id/5.18.0+galaxy1", "5.18.0+galaxy1" ] ], "tutorials": [ [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ] ] }, "ufz/omero_filter/omero_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ufz/omero_filter/omero_filter/5.18.0+galaxy3", "5.18.0+galaxy3" ] ], "tutorials": [ [ "imaging/omero-suite", "Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy", "Imaging", "/topics/imaging/tutorials/omero-suite/tutorial.html" ] ] }, "imgteam/scale_image/ip_scale_image": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/ip_scale_image/0.25.2+galaxy0", "0.25.2+galaxy0" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ] ] }, "imgteam/ridge_filter/ridge_filter_skimage": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/ridge_filter/ridge_filter_skimage/0.22.0+galaxy2", "0.22.0+galaxy2" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ] ] }, "imgteam/highdicom_dicom2tiff/highdicom_dicom2tiff": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/highdicom_dicom2tiff/highdicom_dicom2tiff/0.27.0+galaxy0", "0.27.0+galaxy0" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ] ] }, "imgteam/concat_channels/ip_concat_channels": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/concat_channels/ip_concat_channels/0.5", "0.5" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ] ] }, "imgteam/clip_image/clip_image": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/clip_image/clip_image/0.7.3+galaxy0", "0.7.3+galaxy0" ] ], "tutorials": [ [ "imaging/dicom-anatomical-3d", "Segmentation of Anatomical Structures in Medical 3-D Images", "Imaging", "/topics/imaging/tutorials/dicom-anatomical-3d/tutorial.html" ] ] }, "imgteam/segmetrics/ip_segmetrics": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/segmetrics/ip_segmetrics/1.4.0-2", "1.4.0-2" ] ], "tutorials": [ [ "imaging/parameter-tuning", "Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy", "Imaging", "/topics/imaging/tutorials/parameter-tuning/tutorial.html" ] ] }, "imgteam/iscc_sum_verify/iscc_sum_verify": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/iscc_sum_verify/iscc_sum_verify/0.1.0+galaxy1", "0.1.0+galaxy1" ] ], "tutorials": [ [ "imaging/iscc-suite", "Content Tracking and Verification in Galaxy Workflows with ISCC-SUM", "Imaging", "/topics/imaging/tutorials/iscc-suite/tutorial.html" ] ] }, "imgteam/iscc_sum_similarity/iscc_sum_similarity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/iscc_sum_similarity/iscc_sum_similarity/0.1.0+galaxy1", "0.1.0+galaxy1" ] ], "tutorials": [ [ "imaging/iscc-suite", "Content Tracking and Verification in Galaxy Workflows with ISCC-SUM", "Imaging", "/topics/imaging/tutorials/iscc-suite/tutorial.html" ] ] }, "imgteam/iscc_sum/iscc_sum": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/iscc_sum/iscc_sum/0.1.0+galaxy1", "0.1.0+galaxy1" ] ], "tutorials": [ [ "imaging/iscc-suite", "Content Tracking and Verification in Galaxy Workflows with ISCC-SUM", "Imaging", "/topics/imaging/tutorials/iscc-suite/tutorial.html" ] ] }, "imgteam/points_association_nn/ip_points_association_nn": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/points_association_nn/ip_points_association_nn/0.0.3-2", "0.0.3-2" ] ], "tutorials": [ [ "imaging/detection-of-mitoflashes", "Tracking of mitochondria and capturing mitoflashes", "Imaging", "/topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html" ] ] }, "imgteam/curve_fitting/ip_curve_fitting": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/curve_fitting/ip_curve_fitting/0.0.3-2", "0.0.3-2" ] ], "tutorials": [ [ "imaging/detection-of-mitoflashes", "Tracking of mitochondria and capturing mitoflashes", "Imaging", "/topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html" ] ] }, "imgteam/voronoi_tesselation/voronoi_tessellation": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/voronoi_tesselation/voronoi_tessellation/0.22.0+galaxy3", "0.22.0+galaxy3" ] ], "tutorials": [ [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ] ] }, "imgteam/repeat_channels/repeat_channels": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/repeat_channels/repeat_channels/1.26.4+galaxy0", "1.26.4+galaxy0" ] ], "tutorials": [ [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ] ] }, "imgteam/colorize_labels/colorize_labels": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/colorize_labels/colorize_labels/3.2.1+galaxy3", "3.2.1+galaxy3" ] ], "tutorials": [ [ "imaging/voronoi-segmentation", "Voronoi segmentation", "Imaging", "/topics/imaging/tutorials/voronoi-segmentation/tutorial.html" ] ] }, "bgruening/cp_relate_objects/cp_relate_objects": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_measure_texture/cp_measure_texture": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_measure_image_quality/cp_measure_image_quality": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_measure_image_intensity/cp_measure_image_intensity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_measure_granularity/cp_measure_granularity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_mask_image/cp_mask_image": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_image_math/cp_image_math": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0", "0.1.0" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_gray_to_color/cp_gray_to_color": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_display_data_on_image/cp_display_data_on_image": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9+galaxy1", "3.1.9+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9", "3.1.9" ] ], "tutorials": [ [ "imaging/tutorial-CP", "Nucleoli segmentation and feature extraction using CellProfiler", "Imaging", "/topics/imaging/tutorials/tutorial-CP/tutorial.html" ] ] }, "imgteam/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary/20240614+galaxy1", "20240614+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/imgteam/imagej2_analyze_particles_binary/imagej2_analyze_particles_binary/20240614+galaxy0", "20240614+galaxy0" ] ], "tutorials": [ [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ] ] }, "imgteam/histogram_equalization/ip_histogram_equalization": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/histogram_equalization/ip_histogram_equalization/0.25.2+galaxy0", "0.25.2+galaxy0" ] ], "tutorials": [ [ "imaging/stain-quantification-color-deconvolution", "Quantitative Analysis of Histological Staining Using Color Deconvolution", "Imaging", "/topics/imaging/tutorials/stain-quantification-color-deconvolution/tutorial.html" ] ] }, "imgteam/bioformats2raw/bf2raw": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/imgteam/bioformats2raw/bf2raw/0.7.0+galaxy3", "0.7.0+galaxy3" ] ], "tutorials": [ [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "bgruening/cp_sam/cellposesam": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cp_sam/cellposesam/4.0.8+galaxy0", "4.0.8+galaxy0" ] ], "tutorials": [ [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "bgruening/cellpose/cellpose": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cellpose/cellpose/3.1.0+galaxy2", "3.1.0+galaxy2" ] ], "tutorials": [ [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "interactive_tool_ilastik": { "tool_id": [ [ "interactive_tool_ilastik", "interactive_tool_ilastik" ] ], "tutorials": [ [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "interactive_tool_cellprofiler": { "tool_id": [ [ "interactive_tool_cellprofiler", "interactive_tool_cellprofiler" ] ], "tutorials": [ [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "interactive_tool_cellpose": { "tool_id": [ [ "interactive_tool_cellpose", "interactive_tool_cellpose" ] ], "tutorials": [ [ "imaging/where-to-start-bioimaging-galaxy", "Where to start with bioimage analysis in Galaxy", "Imaging", "/topics/imaging/tutorials/where-to-start-bioimaging-galaxy/tutorial.html" ] ] }, "ebi-gxa/seurat_scale_data/seurat_scale_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_run_umap/seurat_run_umap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_run_pca/seurat_run_pca": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_plot/seurat_plot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_normalise_data/seurat_normalise_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_find_neighbours/seurat_find_neighbours": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_find_markers/seurat_find_markers": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_find_clusters/seurat_find_clusters": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/seurat_filter_cells/seurat_filter_cells": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0", "4.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_FilterPlotandExplore_SeuratTools", "Filter, plot, and explore single cell RNA-seq data with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html" ] ] }, "ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6", "0.0.1+galaxy6" ] ], "tutorials": [ [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ] ] }, "ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0", "1.52.0+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ] ] }, "ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0", "1.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ] ] }, "ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2", "1.6.1+galaxy2" ] ], "tutorials": [ [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ] ] }, "bgruening/alevin/alevin": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy2", "1.10.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0", "1.10.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_alevin", "Generating a single cell matrix using Alevin", "Single Cell", "/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html" ] ] }, "iuc/seurat_create/seurat_create": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1", "5.0+galaxy1" ] ], "tutorials": [ [ "single-cell/scrna-seurat-pbmc3k", "Clustering 3K PBMCs with Seurat", "Single Cell", "/topics/single-cell/tutorials/scrna-seurat-pbmc3k/tutorial.html" ] ] }, "iuc/scater_plot_pca/scater_plot_pca": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2", "1.12.2" ] ], "tutorials": [ [ "single-cell/scrna-scater-qc", "Single-cell quality control with scater", "Single Cell", "/topics/single-cell/tutorials/scrna-scater-qc/tutorial.html" ] ] }, "iuc/scater_plot_dist_scatter/scater_plot_dist_scatter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2", "1.12.2" ] ], "tutorials": [ [ "single-cell/scrna-scater-qc", "Single-cell quality control with scater", "Single Cell", "/topics/single-cell/tutorials/scrna-scater-qc/tutorial.html" ] ] }, "iuc/scater_filter/scater_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2", "1.12.2" ] ], "tutorials": [ [ "single-cell/scrna-scater-qc", "Single-cell quality control with scater", "Single Cell", "/topics/single-cell/tutorials/scrna-scater-qc/tutorial.html" ] ] }, "iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2", "1.12.2" ] ], "tutorials": [ [ "single-cell/scrna-scater-qc", "Single-cell quality control with scater", "Single Cell", "/topics/single-cell/tutorials/scrna-scater-qc/tutorial.html" ] ] }, "iuc/raceid_trajectory/raceid_trajectory": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy0", "0.2.3+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ] ] }, "iuc/raceid_inspecttrajectory/raceid_inspecttrajectory": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy0", "0.2.3+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ] ] }, "iuc/raceid_inspectclusters/raceid_inspectclusters": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy0", "0.2.3+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ] ] }, "iuc/raceid_filtnormconf/raceid_filtnormconf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy0", "0.2.3+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ] ] }, "iuc/raceid_clustering/raceid_clustering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy0", "0.2.3+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-raceid", "Downstream Single-cell RNA analysis with RaceID", "Single Cell", "/topics/single-cell/tutorials/scrna-raceid/tutorial.html" ] ] }, "ebi-gxa/monocle3_topmarkers/monocle3_topmarkers": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers/0.1.5+galaxy0", "0.1.5+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "ebi-gxa/monocle3_reducedim/monocle3_reduceDim": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim/0.1.4+galaxy0", "0.1.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "ebi-gxa/monocle3_preprocess/monocle3_preprocess": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_preprocess/monocle3_preprocess/0.1.4+galaxy0", "0.1.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "ebi-gxa/monocle3_plotcells/monocle3_plotCells": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1", "0.1.5+galaxy1" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "ebi-gxa/monocle3_partition/monocle3_partition": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_partition/monocle3_partition/0.1.4+galaxy0", "0.1.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "ebi-gxa/monocle3_ordercells/monocle3_orderCells": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0", "0.1.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "ebi-gxa/monocle3_learngraph/monocle3_learnGraph": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0", "0.1.4+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "ebi-gxa/monocle3_diffexp/monocle3_diffExp": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1", "0.1.4+galaxy1" ] ], "tutorials": [ [ "single-cell/scrna-case_monocle3-trajectories", "Inferring single cell trajectories with Monocle3", "Single Cell", "/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/tutorial.html" ] ] }, "iuc/edger/edger": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5", "3.36.0+galaxy5" ] ], "tutorials": [ [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ] ] }, "ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8", "1.4.0+galaxy8" ] ], "tutorials": [ [ "single-cell/pseudobulk-analysis", "Pseudobulk Analysis with Decoupler and EdgeR", "Single Cell", "/topics/single-cell/tutorials/pseudobulk-analysis/tutorial.html" ] ] }, "ebi-gxa/scanpy_scale_data/scanpy_scale_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "ebi-gxa/scanpy_run_pca/scanpy_run_pca": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "ebi-gxa/scanpy_normalise_data/scanpy_normalise_data": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "ebi-gxa/scanpy_find_markers/scanpy_find_markers": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "ebi-gxa/scanpy_filter_genes/scanpy_filter_genes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9", "1.8.1+galaxy9" ], [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "interactive_tool_cellxgene_vip": { "tool_id": [ [ "interactive_tool_cellxgene_vip", "interactive_tool_cellxgene_vip" ] ], "tutorials": [ [ "single-cell/scrna-case_basic-pipeline", "Filter, plot and explore single-cell RNA-seq data with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html" ] ] }, "bgruening/music_compare/music_compare": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4", "0.1.1+galaxy4" ] ], "tutorials": [ [ "single-cell/bulk-music-4-compare", "Comparing inferred cell compositions using MuSiC deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html" ] ] }, "ebi-gxa/hca_matrix_downloader/hca_matrix_downloader": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/hca_matrix_downloader/hca_matrix_downloader/v0.0.4+galaxy0", "v0.0.4+galaxy0" ] ], "tutorials": [ [ "single-cell/EBI-retrieval", "Importing files from public atlases", "Single Cell", "/topics/single-cell/tutorials/EBI-retrieval/tutorial.html" ] ] }, "ebi-gxa/sceasy_convert/sceasy_convert": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/sceasy_convert/sceasy_convert/0.0.5+galaxy1", "0.0.5+galaxy1" ] ], "tutorials": [ [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "devteam/tabular_to_fastq/tabular_to_fastq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.5", "1.1.5" ] ], "tutorials": [ [ "single-cell/scrna-data-ingest", "Converting between common single cell data formats", "Single Cell", "/topics/single-cell/tutorials/scrna-data-ingest/tutorial.html" ] ] }, "iuc/ggplot2_violin/ggplot2_violin": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_violin/ggplot2_violin/3.4.0+galaxy1", "3.4.0+galaxy1" ] ], "tutorials": [ [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ] ] }, "__DUPLICATE_FILE_TO_COLLECTION__": { "tool_id": [ [ "__DUPLICATE_FILE_TO_COLLECTION__", "__DUPLICATE_FILE_TO_COLLECTION__" ] ], "tutorials": [ [ "single-cell/bulk-deconvolution-evaluate", "Evaluating Reference Data for Bulk RNA Deconvolution", "Single Cell", "/topics/single-cell/tutorials/bulk-deconvolution-evaluate/tutorial.html" ] ] }, "ebi-gxa/scanpy_run_paga/scanpy_run_paga": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_paga/scanpy_run_paga/1.8.1+galaxy9", "1.8.1+galaxy9" ] ], "tutorials": [ [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "ebi-gxa/scanpy_run_fdg/scanpy_run_fdg": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_fdg/scanpy_run_fdg/1.8.1+galaxy9", "1.8.1+galaxy9" ] ], "tutorials": [ [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "ebi-gxa/scanpy_run_dpt/scanpy_run_dpt": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_dpt/scanpy_run_dpt/1.8.1+galaxy9", "1.8.1+galaxy9" ] ], "tutorials": [ [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "ebi-gxa/scanpy_run_diffmap/scanpy_run_diffmap": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_diffmap/scanpy_run_diffmap/1.8.1+galaxy9", "1.8.1+galaxy9" ] ], "tutorials": [ [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory/1.8.1+galaxy9", "1.8.1+galaxy9" ] ], "tutorials": [ [ "single-cell/scrna-case_trajectories", "Inferring single cell trajectories with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.html" ] ] }, "bgruening/music_inspect_eset/music_inspect_eset": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy4", "0.1.1+galaxy4" ] ], "tutorials": [ [ "single-cell/bulk-music", "Bulk RNA Deconvolution with MuSiC", "Single Cell", "/topics/single-cell/tutorials/bulk-music/tutorial.html" ] ] }, "iuc/sinto_fragments/sinto_fragments": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.9.0+galaxy1", "0.9.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.10.1+galaxy0", "0.10.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ] ] }, "iuc/sinto_barcode/sinto_barcode": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.9.0+galaxy1", "0.9.0+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.10.1+galaxy0", "0.10.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ] ] }, "iuc/episcanpy_preprocess/episcanpy_preprocess": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_preprocess/episcanpy_preprocess/0.3.2+galaxy1", "0.3.2+galaxy1" ] ], "tutorials": [ [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ] ] }, "iuc/episcanpy_build_matrix/episcanpy_build_matrix": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1", "0.3.2+galaxy1" ] ], "tutorials": [ [ "single-cell/scatac-preprocessing-tenx", "Pre-processing of 10X Single-Cell ATAC-seq Datasets", "Single Cell", "/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html" ] ] }, "iuc/celltypist/celltypist": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/celltypist/celltypist/1.7.1+galaxy0", "1.7.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-scanpy-pbmc3k", "Clustering 3K PBMCs with Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html" ] ] }, "ebi-gxa/scanpy_regress_variable/scanpy_regress_variable": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0", "1.8.1+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna-case_cell-cycle", "Removing the effects of the cell cycle", "Single Cell", "/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html" ] ] }, "iuc/seurat_integrate/seurat_integrate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seurat_integrate/seurat_integrate/5.0+galaxy0", "5.0+galaxy0" ] ], "tutorials": [ [ "single-cell/scrna_batch_correction", "Batch Correction and Integration with Seurat or Scanpy", "Single Cell", "/topics/single-cell/tutorials/scrna_batch_correction/tutorial.html" ] ] }, "iuc/rna_starsolo/rna_starsolo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1", "2.7.11a+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3", "2.7.10b+galaxy3" ] ], "tutorials": [ [ "single-cell/scrna-preprocessing-tenx", "Pre-processing of 10X Single-Cell RNA Datasets", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html" ] ] }, "ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9", "0.0.1+galaxy9" ] ], "tutorials": [ [ "single-cell/scanpy_parameter_iterator", "Scanpy Parameter Iterator", "Single Cell", "/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html" ] ] }, "iuc/gprofiler_gost/gprofiler_gost": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_gost/gprofiler_gost/0.1.7+galaxy11", "0.1.7+galaxy11" ] ], "tutorials": [ [ "single-cell/GO-enrichment", "GO Enrichment Analysis on Single-Cell RNA-Seq Data", "Single Cell", "/topics/single-cell/tutorials/GO-enrichment/tutorial.html" ] ] }, "devteam/cut_columns/Cut1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/Cut1/1.0.2", "1.0.2" ] ], "tutorials": [ [ "single-cell/scatac-standard-processing-snapatac2", "Single-cell ATAC-seq standard processing with SnapATAC2", "Single Cell", "/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html" ] ] }, "iuc/umi_tools_count/umi_tools_count": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1", "0.5.5.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2", "0.5.3.2" ] ], "tutorials": [ [ "single-cell/scrna-preprocessing", "Pre-processing of Single-Cell RNA Data", "Single Cell", "/topics/single-cell/tutorials/scrna-preprocessing/tutorial.html" ] ] }, "tduigou/selenzy/selenzy-wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0", "0.2.0" ] ], "tutorials": [ [ "synthetic-biology/basic_assembly_analysis", "Designing plasmids encoding predicted pathways by using the BASIC assembly method", "Synthetic Biology", "/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html" ] ] }, "tduigou/rpbasicdesign/rpbasicdesign": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4", "0.3.4" ] ], "tutorials": [ [ "synthetic-biology/basic_assembly_analysis", "Designing plasmids encoding predicted pathways by using the BASIC assembly method", "Synthetic Biology", "/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html" ] ] }, "tduigou/dnabot/dnabot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0", "3.1.0" ] ], "tutorials": [ [ "synthetic-biology/basic_assembly_analysis", "Designing plasmids encoding predicted pathways by using the BASIC assembly method", "Synthetic Biology", "/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html" ] ] }, "tduigou/rpthermo/rpthermo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1", "5.12.1" ] ], "tutorials": [ [ "synthetic-biology/pathway_analysis", "Evaluating and ranking a set of pathways based on multiple metrics", "Synthetic Biology", "/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html" ] ] }, "tduigou/rpscore/rpscore": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1", "5.12.1" ] ], "tutorials": [ [ "synthetic-biology/pathway_analysis", "Evaluating and ranking a set of pathways based on multiple metrics", "Synthetic Biology", "/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html" ] ] }, "tduigou/rpranker/rpranker": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1", "5.12.1" ] ], "tutorials": [ [ "synthetic-biology/pathway_analysis", "Evaluating and ranking a set of pathways based on multiple metrics", "Synthetic Biology", "/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html" ] ] }, "iuc/rpfba/rpfba": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1", "5.12.1" ] ], "tutorials": [ [ "synthetic-biology/pathway_analysis", "Evaluating and ranking a set of pathways based on multiple metrics", "Synthetic Biology", "/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html" ] ] }, "tduigou/rrparser/rrparser": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6", "2.4.6" ] ], "tutorials": [ [ "synthetic-biology/retrosynthesis_analysis", "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools", "Synthetic Biology", "/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html" ] ] }, "tduigou/rpextractsink/rpextractsink": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1", "5.12.1" ] ], "tutorials": [ [ "synthetic-biology/retrosynthesis_analysis", "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools", "Synthetic Biology", "/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html" ] ] }, "tduigou/rpcompletion/rpcompletion": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.2", "5.12.2" ] ], "tutorials": [ [ "synthetic-biology/retrosynthesis_analysis", "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools", "Synthetic Biology", "/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html" ] ] }, "tduigou/rp2paths/rp2paths": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.5.0", "1.5.0" ] ], "tutorials": [ [ "synthetic-biology/retrosynthesis_analysis", "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools", "Synthetic Biology", "/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html" ] ] }, "tduigou/retropath2/retropath2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0", "2.3.0" ] ], "tutorials": [ [ "synthetic-biology/retrosynthesis_analysis", "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools", "Synthetic Biology", "/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html" ] ] }, "tduigou/get_sbml_model/get_sbml_model": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/tduigou/get_sbml_model/get_sbml_model/0.0.1", "0.0.1" ] ], "tutorials": [ [ "synthetic-biology/retrosynthesis_analysis", "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools", "Synthetic Biology", "/topics/synthetic-biology/tutorials/retrosynthesis_analysis/tutorial.html" ] ] }, "mfa_merge": { "tool_id": [ [ "mfa_merge", "mfa_merge" ] ], "tutorials": [ [ "digital-humanities/mfa_tutorial", "Montreal Forced Aligner", "Digital Humanities", "/topics/digital-humanities/tutorials/mfa_tutorial/tutorial.html" ] ] }, "mfa_g2p": { "tool_id": [ [ "mfa_g2p", "mfa_g2p" ] ], "tutorials": [ [ "digital-humanities/mfa_tutorial", "Montreal Forced Aligner", "Digital Humanities", "/topics/digital-humanities/tutorials/mfa_tutorial/tutorial.html" ] ] }, "mfa_find_oovs": { "tool_id": [ [ "mfa_find_oovs", "mfa_find_oovs" ] ], "tutorials": [ [ "digital-humanities/mfa_tutorial", "Montreal Forced Aligner", "Digital Humanities", "/topics/digital-humanities/tutorials/mfa_tutorial/tutorial.html" ] ] }, "mfa_align": { "tool_id": [ [ "mfa_align", "mfa_align" ] ], "tutorials": [ [ "digital-humanities/mfa_tutorial", "Montreal Forced Aligner", "Digital Humanities", "/topics/digital-humanities/tutorials/mfa_tutorial/tutorial.html" ] ] }, "bgruening/whisperx/whisperx": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/whisperx/whisperx/3.4.2+galaxy1", "3.4.2+galaxy1" ] ], "tutorials": [ [ "digital-humanities/Whisper_speech_recognition", "Transcribing Audio and Video files with Automated Speech Recognition", "Digital Humanities", "/topics/digital-humanities/tutorials/Whisper_speech_recognition/tutorial.html" ] ] }, "iuc/raxml/raxml": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2", "8.2.4+galaxy2" ] ], "tutorials": [ [ "evolution/mtb_phylogeny", "Tree thinking for tuberculosis evolution and epidemiology", "Evolution", "/topics/evolution/tutorials/mtb_phylogeny/tutorial.html" ] ] }, "mvdbeek/add_input_name_as_column/addName": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0", "0.2.0" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ] ] }, "iuc/snp_sites/snp_sites": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0", "2.5.1+galaxy0" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ] ] }, "iuc/snp_dists/snp_dists": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.8.2+galaxy0", "0.8.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0", "0.6.3+galaxy0" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ] ] }, "iuc/clustering_from_distmat/clustering_from_distmat": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/clustering_from_distmat/clustering_from_distmat/1.1.1", "1.1.1" ] ], "tutorials": [ [ "evolution/mtb_transmission", "Identifying tuberculosis transmission links: from SNPs to transmission clusters", "Evolution", "/topics/evolution/tutorials/mtb_transmission/tutorial.html" ] ] }, "jay/pdaug_tsvtofasta/pdaug_tsvtofasta": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_tsvtofasta/pdaug_tsvtofasta/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "jay/pdaug_peptide_sequence_analysis/pdaug_peptide_sequence_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_sequence_analysis/pdaug_peptide_sequence_analysis/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "jay/pdaug_peptide_data_access/pdaug_peptide_data_access": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "jay/pdaug_fishers_plot/pdaug_fishers_plot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/peptide-library-data-analysis", "Peptide Library Data Analysis", "Proteomics", "/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html" ] ] }, "galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0", "1.2.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.12.34", "1.12.34" ] ], "tutorials": [ [ "proteomics/encyclopedia", "EncyclopeDIA", "Proteomics", "/topics/proteomics/tutorials/encyclopedia/tutorial.html" ] ] }, "galaxyp/encyclopedia_quantify/encyclopedia_quantify": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0", "1.2.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.12.34", "1.12.34" ] ], "tutorials": [ [ "proteomics/encyclopedia", "EncyclopeDIA", "Proteomics", "/topics/proteomics/tutorials/encyclopedia/tutorial.html" ] ] }, "recetox/bioconductor_scp/bioconductor_scp": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/bioconductor_scp/bioconductor_scp/1.16.0+galaxy0", "1.16.0+galaxy0" ] ], "tutorials": [ [ "proteomics/bioconductor-scp", "Single Cell Proteomics data analysis with bioconductor-scp", "Proteomics", "/topics/proteomics/tutorials/bioconductor-scp/tutorial.html" ] ] }, "proteore/proteore_prot_features/prot_features": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features/prot_features/2019.01.18", "2019.01.18" ] ], "tutorials": [ [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ] ] }, "proteore/proteore_ms_observation_pepatlas/retr_pepatlas1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_ms_observation_pepatlas/retr_pepatlas1/2019.02.01.1", "2019.02.01.1" ] ], "tutorials": [ [ "proteomics/biomarker_selection", "Biomarker candidate identification", "Proteomics", "/topics/proteomics/tutorials/biomarker_selection/tutorial.html" ] ] }, "galaxyp/openms_peakpickerhires/PeakPickerHiRes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0", "2.3.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ] ] }, "galaxyp/openms_msgfplusadapter/MSGFPlusAdapter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ] ] }, "galaxyp/openms_idmerger/IDMerger": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ] ] }, "galaxyp/openms_idfilter/IDFilter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ] ] }, "galaxyp/openms_consensusid/ConsensusID": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.2.0", "2.2.0" ] ], "tutorials": [ [ "proteomics/protein-id-oms", "Peptide and Protein ID using OpenMS tools", "Proteomics", "/topics/proteomics/tutorials/protein-id-oms/tutorial.html" ] ] }, "galaxyp/openms_proteinquantifier/ProteinQuantifier": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0", "2.6+galaxy0" ] ], "tutorials": [ [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_multiplexresolver/MultiplexResolver": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0", "2.5+galaxy0" ] ], "tutorials": [ [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_idmapper/IDMapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0", "2.6+galaxy0" ] ], "tutorials": [ [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_idconflictresolver/IDConflictResolver": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0", "2.6+galaxy0" ] ], "tutorials": [ [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0", "2.6+galaxy0" ] ], "tutorials": [ [ "proteomics/protein-quant-sil", "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)", "Proteomics", "/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" ] ] }, "galaxyp/mz_to_sqlite/mz_to_sqlite": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.1.1+galaxy0", "2.1.1+galaxy0" ] ], "tutorials": [ [ "proteomics/proteogenomics-dbsearch", "Proteogenomics 2: Database Search", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" ] ] }, "galaxyp/validate_fasta_database/validate_fasta_database": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/validate_fasta_database/validate_fasta_database/0.1.5", "0.1.5" ] ], "tutorials": [ [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ] ] }, "galaxyp/fragpipe/fragpipe_manifest_generator": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe_manifest_generator/23.0+galaxy0", "23.0+galaxy0" ] ], "tutorials": [ [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ] ] }, "galaxyp/fragpipe/fragpipe": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/23.0+galaxy0", "23.0+galaxy0" ] ], "tutorials": [ [ "proteomics/neoantigen-fragpipe-discovery", "Neoantigen 2: Database merge and FragPipe discovery", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/tutorial.html" ] ] }, "jay/pdaug_ml_models/pdaug_ml_models": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0", "0.1.0" ] ], "tutorials": [ [ "proteomics/ml-modeling-of-anti-cancer-peptides", "Machine Learning Modeling of Anticancer Peptides", "Proteomics", "/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html" ] ] }, "PeptideIndexer": { "tool_id": [ [ "PeptideIndexer", "PeptideIndexer" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "MzTabExporter": { "tool_id": [ [ "MzTabExporter", "MzTabExporter" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "MSGFPlusAdapter": { "tool_id": [ [ "MSGFPlusAdapter", "MSGFPlusAdapter" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "IDMerger": { "tool_id": [ [ "IDMerger", "IDMerger" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "IDMapper": { "tool_id": [ [ "IDMapper", "IDMapper" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "IDFilter": { "tool_id": [ [ "IDFilter", "IDFilter" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "IDConflictResolver": { "tool_id": [ [ "IDConflictResolver", "IDConflictResolver" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "HighResPrecursorMassCorrector": { "tool_id": [ [ "HighResPrecursorMassCorrector", "HighResPrecursorMassCorrector" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "FileMerger": { "tool_id": [ [ "FileMerger", "FileMerger" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "FileFilter": { "tool_id": [ [ "FileFilter", "FileFilter" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "FeatureFinderMultiplex": { "tool_id": [ [ "FeatureFinderMultiplex", "FeatureFinderMultiplex" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "FalseDiscoveryRate": { "tool_id": [ [ "FalseDiscoveryRate", "FalseDiscoveryRate" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "ConsensusID": { "tool_id": [ [ "ConsensusID", "ConsensusID" ] ], "tutorials": [ [ "proteomics/ntails", "Detection and quantitation of N-termini (degradomics) via N-TAILS", "Proteomics", "/topics/proteomics/tutorials/ntails/tutorial.html" ] ] }, "iuc/select/select": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/select/select/1.0.4", "1.0.4" ] ], "tutorials": [ [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ] ] }, "iuc/cut/cut": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/cut/cut/1.0.2", "1.0.2" ] ], "tutorials": [ [ "proteomics/neoantigen-variant-annotation", "Neoantigen 4: Variant Annotation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-variant-annotation/tutorial.html" ] ] }, "galaxyp/pyprophet_score/pyprophet_score": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2", "2.1.4.2" ] ], "tutorials": [ [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ] ] }, "galaxyp/pyprophet_protein/pyprophet_protein": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0", "2.1.4.0" ] ], "tutorials": [ [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ] ] }, "galaxyp/pyprophet_peptide/pyprophet_peptide": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0", "2.1.4.0" ] ], "tutorials": [ [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ] ] }, "galaxyp/pyprophet_merge/pyprophet_merge": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0", "2.1.4.0" ] ], "tutorials": [ [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ] ] }, "galaxyp/pyprophet_export/pyprophet_export": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1", "2.1.4.1" ] ], "tutorials": [ [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ] ] }, "galaxyp/openms_openswathworkflow/OpenSwathWorkflow": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/3.1+galaxy0", "3.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0", "2.5+galaxy0" ] ], "tutorials": [ [ "proteomics/DIA_Analysis_OSW", "DIA Analysis using OpenSwathWorkflow", "Proteomics", "/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html" ] ] }, "iuc/seq2hla/seq2hla": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seq2hla/seq2hla/2.3+galaxy0", "2.3+galaxy0" ] ], "tutorials": [ [ "proteomics/neoantigen-predicting-hla-binding", "Neoantigen 5a: Predicting HLA Binding", "Proteomics", "/topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html" ] ] }, "iuc/optitype/optitype": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/optitype/optitype/1.3.5+galaxy0", "1.3.5+galaxy0" ] ], "tutorials": [ [ "proteomics/neoantigen-predicting-hla-binding", "Neoantigen 5a: Predicting HLA Binding", "Proteomics", "/topics/proteomics/tutorials/neoantigen-predicting-hla-binding/tutorial.html" ] ] }, "proteore/proteore_reactome/reactome_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2019.03.05", "2019.03.05" ], [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2018.12.12", "2018.12.12" ] ], "tutorials": [ [ "proteomics/proteome_annotation", "Annotating a protein list identified by LC-MS/MS experiments", "Proteomics", "/topics/proteomics/tutorials/proteome_annotation/tutorial.html" ] ] }, "proteore/proteore_clusterprofiler/cluter_profiler": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18", "2019.02.18" ] ], "tutorials": [ [ "proteomics/proteome_annotation", "Annotating a protein list identified by LC-MS/MS experiments", "Proteomics", "/topics/proteomics/tutorials/proteome_annotation/tutorial.html" ] ] }, "iuc/iedb_api/iedb_api": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api/2.15.2", "2.15.2" ] ], "tutorials": [ [ "proteomics/neoantigen-hla-binding-novel-peptides", "Neoantigen 5b: IEDB binding Validated Neopeptides", "Proteomics", "/topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html" ] ] }, "iuc/fasta_slider/fasta_to_tabular": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fasta_slider/fasta_to_tabular/1.1.1", "1.1.1" ] ], "tutorials": [ [ "proteomics/neoantigen-hla-binding-novel-peptides", "Neoantigen 5b: IEDB binding Validated Neopeptides", "Proteomics", "/topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html" ] ] }, "galaxyp/query_tabular/query_tabular": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/query_tabular/query_tabular/3.3.2", "3.3.2" ] ], "tutorials": [ [ "proteomics/neoantigen-hla-binding-novel-peptides", "Neoantigen 5b: IEDB binding Validated Neopeptides", "Proteomics", "/topics/proteomics/tutorials/neoantigen-hla-binding-novel-peptides/tutorial.html" ] ] }, "artbio/concatenate_multiple_datasets/cat_multi_datasets": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3", "1.4.3" ] ], "tutorials": [ [ "proteomics/proteogenomics-dbcreation", "Proteogenomics 1: Database Creation", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" ] ] }, "iuc/concatenate/concatenate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/concatenate/concatenate/1.0.0", "1.0.0" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ] ] }, "galaxyp/sqlite_to_tabular/sqlite_to_tabular": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/sqlite_to_tabular/sqlite_to_tabular/2.0.0", "2.0.0" ] ], "tutorials": [ [ "proteomics/neoantigen-non-reference-database-generation", "Neoantigen 1b: Non-Reference-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-non-reference-database-generation/tutorial.html" ] ] }, "galaxyp/openms_targetedfileconverter/TargetedFileConverter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0", "2.5+galaxy0" ] ], "tutorials": [ [ "proteomics/DIA_lib_OSW", "Library Generation for DIA Analysis", "Proteomics", "/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html" ] ] }, "galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0", "2.5+galaxy0" ] ], "tutorials": [ [ "proteomics/DIA_lib_OSW", "Library Generation for DIA Analysis", "Proteomics", "/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html" ] ] }, "galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.6+galaxy0", "2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0", "2.5+galaxy0" ] ], "tutorials": [ [ "proteomics/DIA_lib_OSW", "Library Generation for DIA Analysis", "Proteomics", "/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html" ] ] }, "galaxyp/diapysef/diapysef": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0", "0.3.5.0" ] ], "tutorials": [ [ "proteomics/DIA_lib_OSW", "Library Generation for DIA Analysis", "Proteomics", "/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html" ] ] }, "PeakPickerHiRes": { "tool_id": [ [ "PeakPickerHiRes", "PeakPickerHiRes" ] ], "tutorials": [ [ "proteomics/protein-id-sg-ps", "Peptide and Protein ID using SearchGUI and PeptideShaker", "Proteomics", "/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html" ] ] }, "FileConverter": { "tool_id": [ [ "FileConverter", "FileConverter" ] ], "tutorials": [ [ "proteomics/protein-id-sg-ps", "Peptide and Protein ID using SearchGUI and PeptideShaker", "Proteomics", "/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html" ] ] }, "galaxyp/openms_decoydatabase/DecoyDatabase": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0", "2.6+galaxy0" ] ], "tutorials": [ [ "proteomics/database-handling", "Protein FASTA Database Handling", "Proteomics", "/topics/proteomics/tutorials/database-handling/tutorial.html" ] ] }, "peterjc/tmhmm_and_signalp/wolf_psort": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.8", "0.0.8" ] ], "tutorials": [ [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ] ] }, "term_id_vs_term_name": { "tool_id": [ [ "term_id_vs_term_name", "term_id_vs_term_name" ] ], "tutorials": [ [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ] ] }, "get_subontology_from": { "tool_id": [ [ "get_subontology_from", "get_subontology_from" ] ], "tutorials": [ [ "proteomics/secretome-prediction", "Secretome Prediction", "Proteomics", "/topics/proteomics/tutorials/secretome-prediction/tutorial.html" ] ] }, "iuc/arriba_get_filters/arriba_get_filters": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/arriba_get_filters/arriba_get_filters/2.4.0+galaxy1", "2.4.0+galaxy1" ] ], "tutorials": [ [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ] ] }, "iuc/arriba/arriba": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/arriba/arriba/2.4.0+galaxy1", "2.4.0+galaxy1" ] ], "tutorials": [ [ "proteomics/neoantigen-fusion-database-generation", "Neoantigen 1a: Fusion-Database-Generation", "Proteomics", "/topics/proteomics/tutorials/neoantigen-fusion-database-generation/tutorial.html" ] ] }, "galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/1.0.0", "1.0.0" ] ], "tutorials": [ [ "proteomics/proteogenomics-novel-peptide-analysis", "Proteogenomics 3: Novel peptide analysis", "Proteomics", "/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html" ] ] }, "galaxyp/flashlfq/flashlfq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0", "1.0.3.0" ] ], "tutorials": [ [ "proteomics/metaquantome-data-creation", "metaQuantome 1: Data creation", "Proteomics", "/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html" ] ] }, "iuc/multigsea/multigsea": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/multigsea/multigsea/1.12.0+galaxy0", "1.12.0+galaxy0" ] ], "tutorials": [ [ "proteomics/multiGSEA-tutorial", "Multiomics data analysis using MultiGSEA", "Proteomics", "/topics/proteomics/tutorials/multiGSEA-tutorial/tutorial.html" ] ] }, "iuc/rapidnj/rapidnj": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2", "2.3.2" ] ], "tutorials": [ [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ] ] }, "iuc/orfipy/orfipy": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/0.0.4+galaxy0", "0.0.4+galaxy0" ] ], "tutorials": [ [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ] ] }, "bgruening/diamond/bg_diamond_view": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0", "2.0.15+galaxy0" ] ], "tutorials": [ [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ] ] }, "bgruening/diamond/bg_diamond_makedb": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/2.0.15+galaxy0", "2.0.15+galaxy0" ] ], "tutorials": [ [ "genome-annotation/gene-centric", "Comparative gene analysis in unannotated genomes", "Genome Annotation", "/topics/genome-annotation/tutorials/gene-centric/tutorial.html" ] ] }, "iuc/mageck_test/mageck_test": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mageck_test/mageck_test/0.5.9.2.1", "0.5.9.2.1" ] ], "tutorials": [ [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ] ] }, "iuc/mageck_mle/mageck_mle": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.9.2.1", "0.5.9.2.1" ] ], "tutorials": [ [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ] ] }, "iuc/mageck_count/mageck_count": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.9.2.4", "0.5.9.2.4" ] ], "tutorials": [ [ "genome-annotation/crispr-screen", "CRISPR screen analysis", "Genome Annotation", "/topics/genome-annotation/tutorials/crispr-screen/tutorial.html" ] ] }, "iuc/gecko/gecko": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2", "1.2" ] ], "tutorials": [ [ "genome-annotation/hpc-for-lsgc", "From small to large-scale genome comparison", "Genome Annotation", "/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html" ] ] }, "iuc/bp_genbank2gff3/bp_genbank2gff3": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.1", "1.1" ] ], "tutorials": [ [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "cpt/cpt_gbk_to_gff/edu.tamu.cpt.gff3.customGbkToGff": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/cpt/cpt_gbk_to_gff/edu.tamu.cpt.gff3.customGbkToGff/20.1.0.0", "20.1.0.0" ] ], "tutorials": [ [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "bgruening/simsearch/ctb_simsearch": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2", "0.2" ] ], "tutorials": [ [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "bgruening/openbabel_remduplicates/openbabel_remDuplicates": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates/3.1.1+galaxy0", "3.1.1+galaxy0" ] ], "tutorials": [ [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "bgruening/antismash/antismash": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1", "6.1.1+galaxy1" ] ], "tutorials": [ [ "genome-annotation/secondary-metabolite-discovery", "Secondary metabolite discovery", "Genome Annotation", "/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html" ] ] }, "iuc/feelnc/feelnc": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2.1", "0.2.1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2", "0.2" ] ], "tutorials": [ [ "genome-annotation/lncrna", "Long non-coding RNAs (lncRNAs) annotation with FEELnc", "Genome Annotation", "/topics/genome-annotation/tutorials/lncrna/tutorial.html" ] ] }, "Extract_features1": { "tool_id": [ [ "Extract_features1", "Extract_features1" ] ], "tutorials": [ [ "genome-annotation/lncrna", "Long non-coding RNAs (lncRNAs) annotation with FEELnc", "Genome Annotation", "/topics/genome-annotation/tutorials/lncrna/tutorial.html" ] ] }, "iuc/funannotate_compare/funannotate_compare": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy1", "1.8.15+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0", "1.8.15+galaxy0" ] ], "tutorials": [ [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ] ] }, "iuc/funannotate_annotate/funannotate_annotate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy1", "1.8.15+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0", "1.8.15+galaxy0" ] ], "tutorials": [ [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ] ] }, "iuc/aegean_parseval/aegean_parseval": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0", "0.16.0" ] ], "tutorials": [ [ "genome-annotation/funannotate", "Genome annotation with Funannotate", "Genome Annotation", "/topics/genome-annotation/tutorials/funannotate/tutorial.html" ] ] }, "iuc/plasmidfinder/plasmidfinder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1", "2.1.6+galaxy1" ] ], "tutorials": [ [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ] ] }, "iuc/isescan/isescan": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1", "1.7.2.3+galaxy1" ] ], "tutorials": [ [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ] ] }, "iuc/integron_finder/integron_finder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0", "2.0.5+galaxy0" ] ], "tutorials": [ [ "genome-annotation/bacterial-genome-annotation", "Bacterial Genome Annotation", "Genome Annotation", "/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html" ] ] }, "simon-gladman/fasta_stats/fasta-stats": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0", "1.0.0" ] ], "tutorials": [ [ "genome-annotation/annotation-with-maker-short", "Genome annotation with Maker (short)", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html" ] ] }, "gga/apollo_list_organism/list_organism": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1", "3.1" ] ], "tutorials": [ [ "genome-annotation/apollo", "Refining Genome Annotations with Apollo (prokaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo/tutorial.html" ] ] }, "gga/apollo_create_account/create_account": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1", "3.1" ] ], "tutorials": [ [ "genome-annotation/apollo", "Refining Genome Annotations with Apollo (prokaryotes)", "Genome Annotation", "/topics/genome-annotation/tutorials/apollo/tutorial.html" ] ] }, "iuc/red/red": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1", "2018.09.10+galaxy1" ] ], "tutorials": [ [ "genome-annotation/repeatmasker", "Masking repeats with RepeatMasker", "Genome Annotation", "/topics/genome-annotation/tutorials/repeatmasker/tutorial.html" ] ] }, "csbl/repeatmodeler/repeatmodeler": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1", "2.0.4+galaxy1" ] ], "tutorials": [ [ "genome-annotation/repeatmasker", "Masking repeats with RepeatMasker", "Genome Annotation", "/topics/genome-annotation/tutorials/repeatmasker/tutorial.html" ] ] }, "iuc/snap_training/snap_training": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1", "2013_11_29+galaxy1" ] ], "tutorials": [ [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ] ] }, "bgruening/augustus_training/augustus_training": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3", "3.3.3" ] ], "tutorials": [ [ "genome-annotation/annotation-with-maker", "Genome annotation with Maker", "Genome Annotation", "/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html" ] ] }, "iuc/circos/circos_wiggle_to_scatter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy9", "0.69.8+galaxy9" ] ], "tutorials": [ [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "iuc/circos/circos_interval_to_tile": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy9", "0.69.8+galaxy9" ] ], "tutorials": [ [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "iuc/circos/circos_interval_to_text": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy9", "0.69.8+galaxy9" ] ], "tutorials": [ [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "iuc/circos/circos_gc_skew": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy9", "0.69.8+galaxy9" ] ], "tutorials": [ [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "gff2bed1": { "tool_id": [ [ "gff2bed1", "gff2bed1" ] ], "tutorials": [ [ "visualisation/circos-microbial", "Ploting a Microbial Genome with Circos", "Visualisation", "/topics/visualisation/tutorials/circos-microbial/tutorial.html" ] ] }, "iuc/heinz/heinz_visualization": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0", "0.1.0" ] ], "tutorials": [ [ "transcriptomics/network-analysis-with-heinz", "Network analysis with Heinz", "Transcriptomics", "/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html" ] ] }, "iuc/heinz/heinz_scoring": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0", "1.0" ] ], "tutorials": [ [ "transcriptomics/network-analysis-with-heinz", "Network analysis with Heinz", "Transcriptomics", "/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html" ] ] }, "iuc/heinz/heinz_bum": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0", "1.0" ] ], "tutorials": [ [ "transcriptomics/network-analysis-with-heinz", "Network analysis with Heinz", "Transcriptomics", "/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html" ] ] }, "iuc/heinz/heinz": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0", "1.0" ] ], "tutorials": [ [ "transcriptomics/network-analysis-with-heinz", "Network analysis with Heinz", "Transcriptomics", "/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html" ] ] }, "iuc/bedtools/bedtools_bamtofastq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0", "2.24.0" ] ], "tutorials": [ [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ] ] }, "devteam/samtool_filter2/samtool_filter2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2", "1.1.2" ] ], "tutorials": [ [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ] ] }, "devteam/fastq_manipulation/fastq_manipulation": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1", "1.0.1" ] ], "tutorials": [ [ "transcriptomics/srna", "Differential abundance testing of small RNAs", "Transcriptomics", "/topics/transcriptomics/tutorials/srna/tutorial.html" ] ] }, "rnateam/rcas/rcas": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4", "1.5.4" ] ], "tutorials": [ [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "rnateam/peakachu/peakachu": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2", "0.1.0.2" ] ], "tutorials": [ [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "iuc/umi_tools_dedup/umi_tools_dedup": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2", "1.1.2+galaxy2" ] ], "tutorials": [ [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "iuc/bedtools/bedtools_slopbed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1", "2.30.0+galaxy1" ] ], "tutorials": [ [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "iuc/bedtools/bedtools_genomecoveragebed_bedgraph": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0", "2.19.0" ] ], "tutorials": [ [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2", "0.2.2" ] ], "tutorials": [ [ "transcriptomics/clipseq", "CLIP-Seq data analysis from pre-processing to motif detection", "Transcriptomics", "/topics/transcriptomics/tutorials/clipseq/tutorial.html" ] ] }, "rnateam/targetfinder/targetfinder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1", "1.7.0+galaxy1" ] ], "tutorials": [ [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ] ] }, "rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0", "2.0.0" ] ], "tutorials": [ [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ] ] }, "rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0.8.1", "2.0.0.8.1" ] ], "tutorials": [ [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ] ] }, "peterjc/sample_seqs/sample_seqs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.6", "0.2.6" ] ], "tutorials": [ [ "transcriptomics/mirna-target-finder", "Whole transcriptome analysis of Arabidopsis thaliana", "Transcriptomics", "/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html" ] ] }, "rnateam/blockclust/blockclust": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0", "1.1.0" ] ], "tutorials": [ [ "transcriptomics/small_ncrna_clustering", "Small Non-coding RNA Clustering using BlockClust", "Transcriptomics", "/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html" ] ] }, "rnateam/blockbuster/blockbuster": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2", "0.1.2" ] ], "tutorials": [ [ "transcriptomics/small_ncrna_clustering", "Small Non-coding RNA Clustering using BlockClust", "Transcriptomics", "/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html" ] ] }, "iuc/trinotate/trinotate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.1.1", "3.1.1" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_samples_qccheck/trinity_samples_qccheck": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_run_de_analysis/trinity_run_de_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_filter_low_expr_transcripts/trinity_filter_low_expr_transcripts": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_filter_low_expr_transcripts/trinity_filter_low_expr_transcripts/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_define_clusters_by_cutting_tree/trinity_define_clusters_by_cutting_tree": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_define_clusters_by_cutting_tree/trinity_define_clusters_by_cutting_tree/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/trinity/trinity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/transdecoder/transdecoder": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1", "3.0.1" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "iuc/describe_samples/describe_samples": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4", "2.8.4" ] ], "tutorials": [ [ "transcriptomics/full-de-novo", "De novo transcriptome assembly, annotation, and differential expression analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/full-de-novo/tutorial.html" ] ] }, "nilesh/rseqc/rseqc_junction_saturation": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0", "5.0.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "nilesh/rseqc/rseqc_junction_annotation": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0", "5.0.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "nilesh/rseqc/rseqc_inner_distance": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.3+galaxy0", "5.0.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/rnaquast/rna_quast": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.3+galaxy0", "2.2.3+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.1", "2.2.1" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/isoformswitchanalyzer/isoformswitchanalyzer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5", "1.20.0+galaxy5" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "bgruening/text_processing/tp_uniq_tool": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1", "9.3+galaxy1" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "bgruening/pfamscan/pfamscan": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/pfamscan/pfamscan/1.6+galaxy0", "1.6+galaxy0" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "bgruening/cpat/cpat": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.5+galaxy1", "3.0.5+galaxy1" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.4+galaxy0", "3.0.4+galaxy0" ] ], "tutorials": [ [ "transcriptomics/differential-isoform-expression", "Genome-wide alternative splicing analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html" ] ] }, "iuc/goslimmer/goslimmer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1", "1.0.1" ] ], "tutorials": [ [ "transcriptomics/goenrichment", "GO Enrichment Analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/goenrichment/tutorial.html" ] ] }, "iuc/fgsea/fgsea": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1", "1.8.0+galaxy1" ] ], "tutorials": [ [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ] ] }, "iuc/egsea/egsea": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0", "1.20.0" ] ], "tutorials": [ [ "transcriptomics/rna-seq-genes-to-pathways", "3: RNA-seq genes to pathways", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html" ] ] }, "iuc/chira_quantify/chira_quantify": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0", "1.4.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ] ] }, "iuc/chira_merge/chira_merge": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0", "1.4.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ] ] }, "iuc/chira_map/chira_map": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0", "1.4.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ] ] }, "iuc/chira_extract/chira_extract": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0", "1.4.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ] ] }, "iuc/chira_collapse/chira_collapse": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0", "1.4.3+galaxy0" ] ], "tutorials": [ [ "transcriptomics/rna-interactome", "RNA-RNA interactome data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/rna-interactome/tutorial.html" ] ] }, "simon-gladman/velvetoptimiser/velvetoptimiser": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6", "2.2.6" ] ], "tutorials": [ [ "assembly/debruijn-graph-assembly", "De Bruijn Graph Assembly", "Assembly", "/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html" ] ] }, "nml/spades/spades": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/4.2.0+galaxy0", "4.2.0+galaxy0" ] ], "tutorials": [ [ "assembly/debruijn-graph-assembly", "De Bruijn Graph Assembly", "Assembly", "/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html" ] ] }, "iuc/shovill/shovill": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2", "1.1.0+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1", "1.1.0+galaxy1" ] ], "tutorials": [ [ "assembly/mrsa-illumina", "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data", "Assembly", "/topics/assembly/tutorials/mrsa-illumina/tutorial.html" ] ] }, "iuc/yahs/yahs": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1", "1.2a.2+galaxy1" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "iuc/salsa/salsa": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2", "2.3+galaxy2" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "iuc/purge_dups/purge_dups": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0", "1.2.6+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4", "1.2.5+galaxy4" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "bgruening/bionano_scaffold/bionano_scaffold": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3", "3.7.0+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0", "3.7.0+galaxy0" ] ], "tutorials": [ [ "assembly/vgp_genome_assembly", "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step", "Assembly", "/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html" ] ] }, "iuc/parse_mito_blast/parse_mito_blast": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0", "1.0.2+galaxy0" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ] ] }, "devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2", "2.14.1+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1", "2.14.1+galaxy1" ] ], "tutorials": [ [ "assembly/assembly-decontamination", "Decontamination of a genome assembly", "Assembly", "/topics/assembly/tutorials/assembly-decontamination/tutorial.html" ] ] }, "galaxy-australia/smudgeplot/smudgeplot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2", "0.2.5+galaxy+2" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ] ] }, "bgruening/blobtoolkit/blobtoolkit": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2", "4.0.7+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/3.4.0+galaxy0", "3.4.0+galaxy0" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ] ] }, "interactive_tool_blobtoolkit": { "tool_id": [ [ "interactive_tool_blobtoolkit", "interactive_tool_blobtoolkit" ] ], "tutorials": [ [ "assembly/ERGA-post-assembly-QC", "ERGA post-assembly QC", "Assembly", "/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html" ] ] }, "iuc/polypolish/polypolish": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2", "0.5.0+galaxy2" ] ], "tutorials": [ [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ] ] }, "iuc/filtlong/filtlong": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0", "0.2.1+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0", "0.2.0" ] ], "tutorials": [ [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ] ] }, "CONVERTER_bz2_to_uncompressed": { "tool_id": [ [ "CONVERTER_bz2_to_uncompressed", "CONVERTER_bz2_to_uncompressed" ] ], "tutorials": [ [ "assembly/mrsa-nanopore", "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)", "Assembly", "/topics/assembly/tutorials/mrsa-nanopore/tutorial.html" ] ] }, "iuc/circos/circos_interval_to_tiles": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tiles/0.69.8+galaxy7", "0.69.8+galaxy7" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ] ] }, "iuc/circos/circos_aln_to_links": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7", "0.69.8+galaxy7" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ] ] }, "iuc/bedtools/bedtools_complementbed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0", "2.27.0.0" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ] ] }, "devteam/lastz/lastz_wrapper_2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2", "1.3.2" ] ], "tutorials": [ [ "assembly/ecoli_comparison", "Making sense of a newly assembled genome", "Assembly", "/topics/assembly/tutorials/ecoli_comparison/tutorial.html" ] ] }, "iuc/seqtk/seqtk_sample": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2", "1.3.2" ] ], "tutorials": [ [ "assembly/assembly-with-preprocessing", "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads", "Assembly", "/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html" ] ] }, "iuc/compress_file/compress_file": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0", "0.1.0" ] ], "tutorials": [ [ "assembly/mitochondrion-assembly", "Assembly of the mitochondrial genome from PacBio HiFi reads", "Assembly", "/topics/assembly/tutorials/mitochondrion-assembly/tutorial.html" ] ] }, "bgruening/mitohifi/mitohifi": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0", "3.2.3+galaxy0" ] ], "tutorials": [ [ "assembly/mitochondrion-assembly", "Assembly of the mitochondrial genome from PacBio HiFi reads", "Assembly", "/topics/assembly/tutorials/mitochondrion-assembly/tutorial.html" ] ] }, "iuc/iwtomics_testandplot/iwtomics_testandplot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0", "1.0.0.0" ] ], "tutorials": [ [ "statistics/iwtomics", "Interval-Wise Testing for omics data", "Statistics and machine learning", "/topics/statistics/tutorials/iwtomics/tutorial.html" ] ] }, "iuc/iwtomics_plotwithscale/iwtomics_plotwithscale": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_plotwithscale/iwtomics_plotwithscale/1.0.0.0", "1.0.0.0" ] ], "tutorials": [ [ "statistics/iwtomics", "Interval-Wise Testing for omics data", "Statistics and machine learning", "/topics/statistics/tutorials/iwtomics/tutorial.html" ] ] }, "iuc/iwtomics_loadandplot/iwtomics_loadandplot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0", "1.0.0.0" ] ], "tutorials": [ [ "statistics/iwtomics", "Interval-Wise Testing for omics data", "Statistics and machine learning", "/topics/statistics/tutorials/iwtomics/tutorial.html" ] ] }, "paulo_lyra_jr/pycaret_model_comparison/PyCaret_Model_Comparison": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/paulo_lyra_jr/pycaret_model_comparison/PyCaret_Model_Comparison/2024.3.3.2+0", "2024.3.3.2+0" ] ], "tutorials": [ [ "statistics/loris_model", "Galaxy Tabular Learner - Building a Model using Chowell clinical data", "Statistics and machine learning", "/topics/statistics/tutorials/loris_model/tutorial.html" ] ] }, "goeckslab/tabular_learner/tabular_learner": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/tabular_learner/tabular_learner/0.1.3", "0.1.3" ] ], "tutorials": [ [ "statistics/loris_model", "Galaxy Tabular Learner - Building a Model using Chowell clinical data", "Statistics and machine learning", "/topics/statistics/tutorials/loris_model/tutorial.html" ] ] }, "vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_visualize_decisions/pancancer_visualize_decisions": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_visualize_decisions/pancancer_visualize_decisions/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_map_mutation_class/pancancer_map_mutation_class": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_map_mutation_class/pancancer_map_mutation_class/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_compare_within_models/pancancer_compare_within_models": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_compare_within_models/pancancer_compare_within_models/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_classifier/pancancer_classifier": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_classifier/pancancer_classifier/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_apply_weights/pancancer_apply_weights": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_apply_weights/pancancer_apply_weights/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper/0.1.9", "0.1.9" ] ], "tutorials": [ [ "statistics/aberrant_pi3k_pathway_analysis", "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis", "Statistics and machine learning", "/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html" ] ] }, "bgruening/tabpfn/tabpfn": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/tabpfn/tabpfn/2.0.9+galaxy0", "2.0.9+galaxy0" ] ], "tutorials": [ [ "statistics/flexynesis_classification", "Modeling Breast Cancer Subtypes with Flexynesis", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_classification/tutorial.html" ] ] }, "paulo_lyra_jr/ludwig_applications/ludwig_experiment": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/paulo_lyra_jr/ludwig_applications/ludwig_experiment/2024.0.10.3", "2024.0.10.3" ] ], "tutorials": [ [ "statistics/galaxy-ludwig", "Train and Test a Deep learning image classifier with Galaxy-Ludwig", "Statistics and machine learning", "/topics/statistics/tutorials/galaxy-ludwig/tutorial.html" ] ] }, "iuc/pubmed_by_queries/pubmed_by_queries": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pubmed_by_queries/pubmed_by_queries/0.0.2", "0.0.2" ] ], "tutorials": [ [ "statistics/text-mining_simtext", "Text-mining with the SimText toolset", "Statistics and machine learning", "/topics/statistics/tutorials/text-mining_simtext/tutorial.html" ] ] }, "iuc/pmids_to_pubtator_matrix/pmids_to_pubtator_matrix": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pmids_to_pubtator_matrix/pmids_to_pubtator_matrix/0.0.2", "0.0.2" ] ], "tutorials": [ [ "statistics/text-mining_simtext", "Text-mining with the SimText toolset", "Statistics and machine learning", "/topics/statistics/tutorials/text-mining_simtext/tutorial.html" ] ] }, "interactive_tool_simtext_app": { "tool_id": [ [ "interactive_tool_simtext_app", "interactive_tool_simtext_app" ] ], "tutorials": [ [ "statistics/text-mining_simtext", "Text-mining with the SimText toolset", "Statistics and machine learning", "/topics/statistics/tutorials/text-mining_simtext/tutorial.html" ] ] }, "bgruening/flexynesis_cbioportal_import/flexynesis_cbioportal_import": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_cbioportal_import/flexynesis_cbioportal_import/0.2.20+galaxy3", "0.2.20+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_cbioportal_import/flexynesis_cbioportal_import/0.2.20+galaxy1", "0.2.20+galaxy1" ] ], "tutorials": [ [ "statistics/flexynesis_cbio_import", "Prepare Data from CbioPortal for Flexynesis Integration", "Statistics and machine learning", "/topics/statistics/tutorials/flexynesis_cbio_import/tutorial.html" ] ] }, "goeckslab/multimodal_learner/multimodal_learner": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/goeckslab/multimodal_learner/multimodal_learner/0.1.5", "0.1.5" ], [ "toolshed.g2.bx.psu.edu/repos/goeckslab/multimodal_learner/multimodal_learner/0.1.0", "0.1.0" ] ], "tutorials": [ [ "statistics/multimodal_learner", "Gleam Multimodal Learner - Head and Neck cancer Recurrence Prediction with HANCOCK", "Statistics and machine learning", "/topics/statistics/tutorials/multimodal_learner/tutorial.html" ] ] }, "bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1", "0.1" ] ], "tutorials": [ [ "statistics/age-prediction-with-ml", "Age prediction using machine learning", "Statistics and machine learning", "/topics/statistics/tutorials/age-prediction-with-ml/tutorial.html" ] ] }, "bgruening/sklearn_nn_classifier/sklearn_nn_classifier": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/1.0.11.0", "1.0.11.0" ] ], "tutorials": [ [ "statistics/classification_machinelearning", "Classification in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/classification_machinelearning/tutorial.html" ] ] }, "recetox/xtb_molecular_optimization/xtb_molecular_optimization": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy3", "6.6.1+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy1", "6.6.1+galaxy1" ] ], "tutorials": [ [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ] ] }, "recetox/qcxms_production_run/qcxms_production_run": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy3", "5.2.1+galaxy3" ] ], "tutorials": [ [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ] ] }, "recetox/qcxms_neutral_run/qcxms_neutral_run": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy4", "5.2.1+galaxy4" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy3", "5.2.1+galaxy3" ] ], "tutorials": [ [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ] ] }, "recetox/qcxms_getres/qcxms_getres": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/5.2.1+galaxy2", "5.2.1+galaxy2" ] ], "tutorials": [ [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ] ] }, "bgruening/ctb_im_conformers/ctb_im_conformers": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_conformers/ctb_im_conformers/1.1.4+galaxy0", "1.1.4+galaxy0" ] ], "tutorials": [ [ "metabolomics/qcxms-predictions", "Predicting EI+ mass spectra with QCxMS", "Metabolomics", "/topics/metabolomics/tutorials/qcxms-predictions/tutorial.html" ] ] }, "galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3", "1.18.0.3" ] ], "tutorials": [ [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.4", "1.18.0.4" ] ], "tutorials": [ [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "galaxyp/cardinal_segmentations/cardinal_segmentations": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3", "1.12.1.3" ] ], "tutorials": [ [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "galaxyp/cardinal_preprocessing/cardinal_preprocessing": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3", "1.12.1.3" ] ], "tutorials": [ [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "galaxyp/cardinal_combine/cardinal_combine": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3", "1.12.1.3" ] ], "tutorials": [ [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "galaxyp/cardinal_classification/cardinal_classification": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3", "1.12.1.3" ] ], "tutorials": [ [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1", "1.0.1" ] ], "tutorials": [ [ "metabolomics/msi-finding-nglycans", "Mass spectrometry imaging: Finding differential analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html" ] ] }, "recetox/waveica/waveica": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/waveica/waveica/0.2.0+galaxy2", "0.2.0+galaxy2" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ] ] }, "recetox/riassigner/riassigner": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1", "0.3.4+galaxy1" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ] ] }, "recetox/ramclustr_define_experiment/ramclustr_define_experiment": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr_define_experiment/ramclustr_define_experiment/1.0.2", "1.0.2" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ] ] }, "recetox/ramclustr/ramclustr": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.3.0+galaxy0", "1.3.0+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2", "1.2.4+galaxy2" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ] ] }, "recetox/matchms_similarity/matchms_similarity": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0", "0.20.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ] ] }, "recetox/matchms_formatter/matchms_formatter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0", "0.20.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ] ] }, "recetox/matchms_filtering/matchms_filtering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/matchms_filtering/matchms_filtering/0.17.0+galaxy0", "0.17.0+galaxy0" ] ], "tutorials": [ [ "metabolomics/gc_ms_with_xcms", "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)", "Metabolomics", "/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html" ] ] }, "fgiacomoni/hmdb_ms_search/wsdl_hmdb": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/wsdl_hmdb/2018-10-01", "2018-10-01" ], [ "toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/wsdl_hmdb/1.7.6", "1.7.6" ] ], "tutorials": [ [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ] ] }, "ethevenot/univariate/Univariate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4", "2.2.4" ] ], "tutorials": [ [ "metabolomics/lcms", "Mass spectrometry: LC-MS analysis", "Metabolomics", "/topics/metabolomics/tutorials/lcms/tutorial.html" ] ] }, "galaxyp/cardinal_spectra_plots/cardinal_spectra_plots": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.3", "2.6.0.3" ], [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0", "2.6.0.0" ] ], "tutorials": [ [ "metabolomics/msi-analyte-distribution", "Mass spectrometry imaging: Examining the spatial distribution of analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html" ] ] }, "galaxyp/cardinal_filtering/cardinal_filtering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0", "2.6.0.0" ] ], "tutorials": [ [ "metabolomics/msi-analyte-distribution", "Mass spectrometry imaging: Examining the spatial distribution of analytes", "Metabolomics", "/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html" ] ] }, "recetox/mfassignr_snplot/mfassignr_snplot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_snplot/mfassignr_snplot/1.1.2+galaxy0", "1.1.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_snplot/mfassignr_snplot/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_recallist/mfassignr_recallist": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_recallist/mfassignr_recallist/1.1.2+galaxy0", "1.1.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_recallist/mfassignr_recallist/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_recal/mfassignr_recal": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_recal/mfassignr_recal/1.1.2+galaxy0", "1.1.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_recal/mfassignr_recal/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_mfassigncho/mfassignr_mfassignCHO": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_mfassigncho/mfassignr_mfassignCHO/1.1.2+galaxy0", "1.1.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_mfassigncho/mfassignr_mfassignCHO/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_mfassign/mfassignr_mfassign": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_mfassign/mfassignr_mfassign/1.1.2+galaxy0", "1.1.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_mfassign/mfassignr_mfassign/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_kmdnoise/mfassignr_kmdnoise": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_kmdnoise/mfassignr_kmdnoise/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_isofiltr/mfassignr_isofiltr": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_isofiltr/mfassignr_isofiltr/1.1.2+galaxy0", "1.1.2+galaxy0" ], [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_isofiltr/mfassignr_isofiltr/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_histnoise/mfassignr_kmdnoise": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_histnoise/mfassignr_kmdnoise/1.1.2+galaxy0", "1.1.2+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_histnoise/mfassignr_histnoise": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_histnoise/mfassignr_histnoise/1.1.1+galaxy0", "1.1.1+galaxy0" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "recetox/mfassignr_findrecalseries/mfassignr_findRecalSeries": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_findrecalseries/mfassignr_findRecalSeries/1.1.2+galaxy1", "1.1.2+galaxy1" ] ], "tutorials": [ [ "metabolomics/mfassignr", "Molecular formula assignment and mass recalibration with MFAssignR package", "Metabolomics", "/topics/metabolomics/tutorials/mfassignr/tutorial.html" ] ] }, "iuc/geneiobio/gene_iobio_display_generation_iframe": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1", "4.7.1" ] ], "tutorials": [ [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/ega_download_client/pyega3": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0", "5.0.2+galaxy0" ] ], "tutorials": [ [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "iuc/bcftools_merge/bcftools_merge": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10", "1.10" ] ], "tutorials": [ [ "variant-analysis/trio-analysis", "Trio Analysis using Synthetic Datasets from RD-Connect GPAP", "Variant Analysis", "/topics/variant-analysis/tutorials/trio-analysis/tutorial.html" ] ] }, "wolma/mimodd_main/mimodd_vcf_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1", "0.1.8_1" ] ], "tutorials": [ [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ] ] }, "wolma/mimodd_main/mimodd_varreport": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1", "0.1.8_1" ] ], "tutorials": [ [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ] ] }, "wolma/mimodd_main/mimodd_varextract": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1", "0.1.8_1" ] ], "tutorials": [ [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ] ] }, "wolma/mimodd_main/mimodd_varcall": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1", "0.1.8_1" ] ], "tutorials": [ [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ] ] }, "wolma/mimodd_main/mimodd_map": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1", "0.1.8_1" ] ], "tutorials": [ [ "variant-analysis/mapping-by-sequencing", "Mapping and molecular identification of phenotype-causing mutations", "Variant Analysis", "/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html" ] ] }, "wolma/mimodd_main/mimodd_info": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1", "0.1.8_1" ] ], "tutorials": [ [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "iuc/ucsc_fatovcf/fatovcf": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fatovcf/fatovcf/426+galaxy0", "426+galaxy0" ] ], "tutorials": [ [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "iuc/samtools_merge/samtools_merge": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0", "1.15.1+galaxy0" ] ], "tutorials": [ [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "iuc/ivar_trim/ivar_trim": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0", "1.4.2+galaxy0" ] ], "tutorials": [ [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "devteam/emboss_5/EMBOSS: maskseq51": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0", "5.0.0" ] ], "tutorials": [ [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "__APPLY_RULES__": { "tool_id": [ [ "__APPLY_RULES__", "__APPLY_RULES__" ] ], "tutorials": [ [ "variant-analysis/pox-tiled-amplicon", "Pox virus genome analysis from tiled-amplicon sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html" ] ] }, "iuc/varscan_somatic/varscan_somatic": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6", "2.4.3.6" ] ], "tutorials": [ [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "iuc/gemini_annotate/gemini_annotate": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2", "0.20.1+galaxy2" ] ], "tutorials": [ [ "variant-analysis/somatic-variants", "Identification of somatic and germline variants from tumor and normal sample pairs", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variants/tutorial.html" ] ] }, "devteam/vcffilter/vcffilter2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3", "1.0.0_rc3+galaxy3" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy3", "1.0.0_rc1+galaxy3" ] ], "tutorials": [ [ "variant-analysis/non-dip", "Calling variants in non-diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/non-dip/tutorial.html" ] ] }, "iuc/bcftools_mpileup/bcftools_mpileup": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_mpileup/bcftools_mpileup/1.15.1+galaxy4", "1.15.1+galaxy4" ] ], "tutorials": [ [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ] ] }, "iuc/bcftools_call/bcftools_call": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.15.1+galaxy5", "1.15.1+galaxy5" ] ], "tutorials": [ [ "variant-analysis/baculovirus-isolate-variation", "Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates", "Variant Analysis", "/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.html" ] ] }, "iuc/gemini_db_info/gemini_db_info": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1", "0.20.1" ] ], "tutorials": [ [ "variant-analysis/dip", "Calling variants in diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/dip/tutorial.html" ] ] }, "devteam/vcfallelicprimitives/vcfallelicprimitives": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0", "1.0.0_rc3+galaxy0" ] ], "tutorials": [ [ "variant-analysis/dip", "Calling variants in diploid systems", "Variant Analysis", "/topics/variant-analysis/tutorials/dip/tutorial.html" ] ] }, "iuc/tbvcfreport/tbvcfreport": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.1+galaxy0", "1.0.1+galaxy0" ] ], "tutorials": [ [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/mosdepth/mosdepth": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.12+galaxy0", "0.3.12+galaxy0" ] ], "tutorials": [ [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/jvarkit_wgscoverageplotter/jvarkit_wgscoverageplotter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/jvarkit_wgscoverageplotter/jvarkit_wgscoverageplotter/20201223+galaxy0", "20201223+galaxy0" ] ], "tutorials": [ [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "devteam/emboss_5/EMBOSS:%20seqret84": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS:%20seqret84/5.0.0", "5.0.0" ] ], "tutorials": [ [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "devteam/emboss_5/EMBOSS: seqret84": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0", "5.0.0" ] ], "tutorials": [ [ "variant-analysis/tb-variant-analysis", "M. tuberculosis Variant Analysis", "Variant Analysis", "/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html" ] ] }, "iuc/nextclade/nextclade": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0", "2.7.0+galaxy0" ] ], "tutorials": [ [ "variant-analysis/sars-cov-2-variant-discovery", "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data", "Variant Analysis", "/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html" ] ] }, "iuc/control_freec/control_freec": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/11.6+galaxy2", "11.6+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/11.6+galaxy1", "11.6+galaxy1" ] ], "tutorials": [ [ "variant-analysis/somatic-variant-discovery", "Somatic Variant Discovery from WES Data Using Control-FREEC", "Variant Analysis", "/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.html" ] ] }, "iuc/bedtools/bedtools_mergebed": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0", "2.30.0" ] ], "tutorials": [ [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ] ] }, "iuc/bbgbigwig/bbgtobigwig": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/bbgbigwig/bbgtobigwig/0.1", "0.1" ] ], "tutorials": [ [ "epigenetics/formation_of_super-structures_on_xi", "Formation of the Super-Structures on the Inactive X", "Epigenetics", "/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html" ] ] }, "iuc/transit_gumbel/transit_gumbel": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0", "3.0.2+galaxy0" ] ], "tutorials": [ [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ] ] }, "iuc/gff_to_prot/gff_to_prot": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0", "3.0.2+galaxy0" ] ], "tutorials": [ [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ] ] }, "devteam/bowtie_wrappers/bowtie_wrapper": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0", "1.2.0" ] ], "tutorials": [ [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ] ] }, "bgruening/find_subsequences/bg_find_subsequences": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2", "0.2" ] ], "tutorials": [ [ "genome-annotation/tnseq", "Essential genes detection with Transposon insertion sequencing", "Genome Annotation", "/topics/genome-annotation/tutorials/tnseq/tutorial.html" ] ] }, "nick/sequence_content_trimmer/sequence_content_trimmer": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/sequence_content_trimmer/0.2.3", "0.2.3" ], [ "toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/sequence_content_trimmer/0.1", "0.1" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ] ] }, "nick/dunovo/make_families": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/make_families/3.0.2", "3.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/make_families/2.15", "2.15" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ] ] }, "nick/dunovo/dunovo": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/dunovo/3.0.2", "3.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/dunovo/2.15", "2.15" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ] ] }, "nick/dunovo/correct_barcodes": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/3.0.2", "3.0.2" ], [ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.15", "2.15" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ] ] }, "nick/dunovo/align_families": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.15", "2.15" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ] ] }, "nick/allele_counts/allele_counts_1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.3.2", "1.3.2" ], [ "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2", "1.2" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ] ] }, "blankenberg/naive_variant_caller/naive_variant_caller": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.4", "0.0.4" ] ], "tutorials": [ [ "variant-analysis/dunovo", "Calling very rare variants", "Variant Analysis", "/topics/variant-analysis/tutorials/dunovo/tutorial.html" ] ] }, "iuc/pathview/pathview": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0", "1.34.0+galaxy0" ] ], "tutorials": [ [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "iuc/dexseq/dexseq_count": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.28.1.0", "1.28.1.0" ] ], "tutorials": [ [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "iuc/dexseq/dexseq": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy1", "1.28.1+galaxy1" ] ], "tutorials": [ [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "__TAG_FROM_FILE__": { "tool_id": [ [ "__TAG_FROM_FILE__", "__TAG_FROM_FILE__" ] ], "tutorials": [ [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "ChangeCase": { "tool_id": [ [ "ChangeCase", "ChangeCase" ] ], "tutorials": [ [ "transcriptomics/ref-based", "Reference-based RNA-Seq data analysis", "Transcriptomics", "/topics/transcriptomics/tutorials/ref-based/tutorial.html" ] ] }, "bgruening/sklearn_numeric_clustering/sklearn_numeric_clustering": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_numeric_clustering/sklearn_numeric_clustering/1.0.8.1", "1.0.8.1" ] ], "tutorials": [ [ "statistics/clustering_machinelearning", "Clustering in Machine Learning", "Statistics and machine learning", "/topics/statistics/tutorials/clustering_machinelearning/tutorial.html" ] ] }, "saskia-hiltemann/krona_text/krona-text": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1", "1" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ] ] }, "iuc/mothur_make_group/mothur_make_group": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0", "1.36.1.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ] ] }, "iuc/metaphlan2krona/metaphlan2krona": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0", "2.6.0.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ] ] }, "iuc/metaphlan2/metaphlan2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0", "2.6.0.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ] ] }, "iuc/humann2_renorm_table/humann2_renorm_table": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.9.9.0", "0.9.9.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ] ] }, "iuc/humann2_regroup_table/humann2_regroup_table": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann2_regroup_table/humann2_regroup_table/0.9.9.0", "0.9.9.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ] ] }, "iuc/humann2/humann2": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.9.9.0", "0.9.9.0" ] ], "tutorials": [ [ "microbiome/general-tutorial", "Analyses of metagenomics data - The global picture", "Microbiome", "/topics/microbiome/tutorials/general-tutorial/tutorial.html" ] ] }, "devteam/fastq_quality_filter/cshl_fastq_quality_filter": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2+galaxy2", "1.0.2+galaxy2" ], [ "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1", "1.0.1" ] ], "tutorials": [ [ "introduction/galaxy-intro-short", "A short introduction to Galaxy", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-short/tutorial.html" ] ] }, "devteam/get_flanks/get_flanks1": { "tool_id": [ [ "toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0", "1.0.0" ] ], "tutorials": [ [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ] ] }, "CONVERTER_interval_to_bed_0": { "tool_id": [ [ "CONVERTER_interval_to_bed_0", "CONVERTER_interval_to_bed_0" ] ], "tutorials": [ [ "introduction/galaxy-intro-peaks2genes", "From peaks to genes", "Introduction to Galaxy Analyses", "/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html" ] ] } }