Transcriptomics — Community Home
This is a new, experimental "Community Home" for a given topic. It is intended to highlight community contributions over the years to a topic!2024 Year in Review
So many new additions to our community!
1
News
4
Events
1
Tutorials
1
Recordings
4
Workflows
2
Contributors
News
Events
- Workshop on high-throughput sequencing data analysis with Galaxy
- Workshop on high-throughput sequencing data analysis with Galaxy
- Bioconductor Carpentries workshop: Analysis and Interpretation of Bulk RNA-Seq Data
- A practical introduction to bioinformatics and RNA-seq using Galaxy
Tutorials
Recordings
Workflows
- scRNA Plant Analysis
- BY-COVID: Data Download
- mRNA-Seq BY-COVID Pipeline: Counts
- mRNA-Seq BY-COVID Pipeline: Analysis
Contributors
2023 Year in Review
So many new additions to our community!
1
News
4
Tutorials
1
Slides
1
Recordings
4
Workflows
1
Grants
6
Contributors
News
Tutorials
- Genome-wide alternative splicing analysis
- RNA-seq Alignment with STAR
- Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
- Comparing inferred cell compositions using MuSiC deconvolution
Slides
Recordings
Workflows
- Filter, Plot and Explore Single-cell RNA-seq Data updated
- Preprocessing of 10X scRNA-seq data
- GTN_differential_isoform_expression
- Cell Cycle Regression Workflow
Grants
Contributors
2022 Year in Review
So many new additions to our community!
1
News
1
Tutorials
2
Faqs
2
Workflows
4
Contributors
2021 Year in Review
So many new additions to our community!
2
News
2
Tutorials
1
Slides
10
Recordings
7
Faqs
2
Workflows
1
Organisations
1
Contributors
News
- New Tutorial: Visualization of RNA-Seq results with Volcano Plot in R
- New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana
Tutorials
- Visualization of RNA-Seq results with Volcano Plot in R
- Whole transcriptome analysis of Arabidopsis thaliana
Slides
Recordings
- Recording of Whole transcriptome analysis of Arabidopsis thaliana
- Recording of Whole transcriptome analysis of Arabidopsis thaliana
- Recording of Bulk RNA Deconvolution with MuSiC
- Recording of RNA Seq Counts to Viz in R
- Recording of Visualization of RNA-Seq results with Volcano Plot in R
- Recording of Introduction to Transcriptomics
- Recording of Whole transcriptome analysis of Arabidopsis thaliana
- Recording of Visualization of RNA-Seq results with Volcano Plot
- Recording of De novo transcriptome reconstruction with RNA-Seq
- Recording of Reference-based RNA-Seq data analysis
Faqs
- I’m using the same training data, tools, and parameters as the tutorial, but I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
- In 'infer experiments' I get unequal numbers, but in the IGV it looks like it is unstranded. What does this mean?
- RNAstar: Why do we set 36 for 'Length of the genomic sequence around annotated junctions'?
- Is it possible to visualize the RNA STAR bam file using the JBrowse tool?
- When is the "infer experiment" tool used in practice?
- Could I use a different p-adj value for filtering differentially expressed genes?
- The tutorial uses the normalised count table for visualisation. What about using VST normalised counts or rlog normalised counts?
Workflows
Organisations
Contributors
2020 Year in Review
So many new additions to our community!
2
Tutorials
1
Slides
3
Workflows
1
Grants
5
Contributors
Tutorials
Slides
Workflows
Grants
Contributors
2019 Year in Review
So many new additions to our community!
2
Tutorials
8
Workflows
11
Contributors
Tutorials
Workflows
- Scater
- QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows
- DEG Part - Ref Based RNA Seq - Transcriptomics - GTN
- Visualization Of RNA-Seq Results With Volcano Plot
- RaceID Workflow
- CelSeq2: Single Batch (mm10)
- CelSeq2: Multi Batch (mm10)
- GO Enrichment Workflow
Contributors
2018 Year in Review
So many new additions to our community!
8
Tutorials
1
Slides
8
Workflows
13
Contributors
Tutorials
- Visualization of RNA-Seq results with Volcano Plot
- Visualization of RNA-Seq results with heatmap2
- 2: RNA-seq counts to genes
- 3: RNA-seq genes to pathways
- Small Non-coding RNA Clustering using BlockClust
- Network analysis with Heinz
- 1: RNA-Seq reads to counts
- CLIP-Seq data analysis from pre-processing to motif detection
Slides
Workflows
- Heatmap2 Workflow
- RNA Seq Reads To Counts
- RNA Seq Genes To Pathways (imported from uploaded file)
- RNA Seq Counts To Genes
- Blockclust 1.1.0 Clustering
- Workflow Constructed From History 'Heinz Workflow Trial Sep 11'
- De novo transcriptome reconstruction with RNA-Seq
- Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38
Contributors
2017 Year in Review
So many new additions to our community!
3
Tutorials
1
Slides
3
Workflows
21
Contributors
Tutorials
- Visualization of RNA-Seq results with CummeRbund
- Differential abundance testing of small RNAs
- De novo transcriptome reconstruction with RNA-Seq
Slides
Workflows
- rna-seq-viz-with-cummerbund
- sRNA Seq Step 2: Salmon And DESeq2
- sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)
Contributors
2016 Year in Review
So many new additions to our community!
1
Tutorials
1
Slides
Cumulative Data as CSV
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