Nicola Soranzo

Affiliations

Earlham Institute

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Tutorials

Contributing to the Galaxy Training Material / Generating PDF artefacts of the website 🧐
Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
Contributing to the Galaxy Training Material / Running the GTN website locally using the command line 🧐
Contributing to the Galaxy Training Material / Including a new topic 🧐
Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours 🧐
Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
Contributing to the Galaxy Training Material / Contributing with GitHub via its interface 🧐
Contributing to the Galaxy Training Material / Contributing with GitHub via command-line 🧐
Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
Contributing to the Galaxy Training Material / Adding auto-generated video to your slides 🧐
Single Cell / Pre-processing of Single-Cell RNA Data 🧐
Single Cell / Understanding Barcodes 🧐
Single Cell / Clustering 3K PBMCs with Scanpy 🧐
Single Cell / Single-cell quality control with scater ✍️ 🧐
Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 📝
Sequence analysis / Quality Control 🧐
Sequence analysis / Mapping 🧐
Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows 🧐
Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy 🧐
Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐
Using Galaxy and Managing your Data / Using dataset collections 🧐
Using Galaxy and Managing your Data / Rule Based Uploader: Advanced 🧐
Using Galaxy and Managing your Data / Extracting Workflows from Histories 🧐
Proteomics / Proteogenomics 1: Database Creation 🧐
Proteomics / Mass spectrometry imaging: Loading and exploring MSI data 🧐
Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) 🧐
Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS 🧐
Proteomics / Proteogenomics 2: Database Search 🧐
Proteomics / Secretome Prediction 🧐
Proteomics / Peptide and Protein ID using OpenMS tools 🧐
Proteomics / Proteogenomics 3: Novel peptide analysis 🧐
Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method 🧐
Proteomics / Metaproteomics tutorial 🧐
Proteomics / Protein FASTA Database Handling 🧐
Teaching and Hosting Galaxy training / Galaxy Admin Training 🧐
Teaching and Hosting Galaxy training / Set up a Galaxy for Training 🧐
Teaching and Hosting Galaxy training / Running a workshop as instructor 🧐
Assembly / De Bruijn Graph Assembly 🧐
Assembly / An Introduction to Genome Assembly 🧐
Assembly / Making sense of a newly assembled genome 🧐
Assembly / Unicycler Assembly 🧐
Epigenetics / ATAC-Seq data analysis 🧐
Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) 🧐
Epigenetics / Infinium Human Methylation BeadChip 🧐
Epigenetics / Identification of the binding sites of the Estrogen receptor 🧐
Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer 🧐
Epigenetics / DNA Methylation data analysis 🧐
Ecology / RAD-Seq to construct genetic maps 🧐
Ecology / RAD-Seq Reference-based data analysis 🧐
Ecology / RAD-Seq de-novo data analysis 🧐
Microbiome / Analyses of metagenomics data - The global picture 🧐
Microbiome / 16S Microbial Analysis with mothur (extended) 🧐
Genome Annotation / Genome annotation with Prokka 🧐
Genome Annotation / Genome Annotation 🧐
Genome Annotation / Genome annotation with Maker 🧐
Galaxy Server administration / Reference Data with CVMFS without Ansible 🧐
Galaxy Server administration / Galaxy Database schema 🧐
Galaxy Server administration / Data Libraries 🧐
Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
Galaxy Server administration / Reference Data with CVMFS 🧐
Galaxy Server administration / Galaxy Installation with Ansible 📝 🧐
Galaxy Server administration / Galaxy Interactive Tools 🧐
Galaxy Server administration / Automation with Jenkins 🧐
Galaxy Server administration / External Authentication ✍️ 🧐
Galaxy Server administration / Distributed Object Storage 🧐
Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
Galaxy Server administration / Ansible 🧐
Galaxy Server administration / Enable upload via FTP 🧐
Galaxy Server administration / Mapping Jobs to Destinations using TPV 🧐
Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
Galaxy Server administration / Galaxy Monitoring with Reports 🧐
Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
Introduction to Galaxy Analyses / Galaxy Basics for genomics ✍️ 🧐
Introduction to Galaxy Analyses / From peaks to genes ✍️ 🧐
Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐
Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
Introduction to Galaxy Analyses / IGV Introduction 🧐
Introduction to Galaxy Analyses / NGS data logistics 🧐
Introduction to Galaxy Analyses / A short introduction to Galaxy ✍️ 🧐
Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease 🧐
Variant Analysis / Calling very rare variants 🧐
Variant Analysis / Mapping and molecular identification of phenotype-causing mutations 🧐
Variant Analysis / Microbial Variant Calling 🧐
Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis 🧐
Variant Analysis / Calling variants in non-diploid systems 🧐
Variant Analysis / Calling variants in diploid systems ✍️ 🧐
Statistics and machine learning / Interval-Wise Testing for omics data 🧐
FAIR Data, Workflows, and Research / FAIR and its Origins ✍️
FAIR Data, Workflows, and Research / Metadata ✍️
FAIR Data, Workflows, and Research / Access ✍️
FAIR Data, Workflows, and Research / Persistent Identifiers ✍️
FAIR Data, Workflows, and Research / Data Registration ✍️
Transcriptomics / Differential abundance testing of small RNAs 🧐
Transcriptomics / Network analysis with Heinz 🧐
Transcriptomics / Visualization of RNA-Seq results with Volcano Plot 🧐
Transcriptomics / De novo transcriptome reconstruction with RNA-Seq 🧐
Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection 🧐
Transcriptomics / 3: RNA-seq genes to pathways 🧐
Transcriptomics / 1: RNA-Seq reads to counts 🧐
Transcriptomics / 2: RNA-seq counts to genes 🧐
Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
Transcriptomics / Visualization of RNA-Seq results with CummeRbund 🧐
Transcriptomics / Visualization of RNA-Seq results with heatmap2 🧐
Transcriptomics / Reference-based RNAseq data analysis (long) 🧐
Development in Galaxy / Data source integration 🧐
Development in Galaxy / JavaScript plugins 🧐
Development in Galaxy / Generic plugins 🧐
Development in Galaxy / Scripting Galaxy using the API and BioBlend ✍️ 🧐
Development in Galaxy / Galaxy Webhooks 🧐

Slides

Development in Galaxy / Galaxy from a developer point of view 🧐
Contributing to the Galaxy Training Material / Creating Slides 🧐
Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material 🧐
Contributing to the Galaxy Training Material / Contributing with GitHub via command-line 🧐
Sequence analysis / Quality Control 🧐
Sequence analysis / Mapping 🧐
Using Galaxy and Managing your Data / Getting data into Galaxy 🧐
Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 🧐
Assembly / De Bruijn Graph Assembly 🧐
Assembly / An Introduction to Genome Assembly 🧐
Assembly / Unicycler Assembly 🧐
Epigenetics / Introduction to ChIP-Seq data analysis 🧐
Epigenetics / Introduction to DNA Methylation data analysis 🧐
Microbiome / Introduction to Microbiome Analysis 🧐
Genome Annotation / Genome annotation with Prokka 🧐
Galaxy Server administration / Galaxy on the Cloud 🧐
Galaxy Server administration / Terraform 🧐
Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration 🧐
Galaxy Server administration / Controlling Galaxy with systemd or Supervisor 🧐
Galaxy Server administration / Storage Management 🧐
Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
Galaxy Server administration / Reference Data with CVMFS 🧐
Galaxy Server administration / Galaxy Installation with Ansible 🧐
Galaxy Server administration / Gearing towards production 🧐
Galaxy Server administration / Galaxy Interactive Tools 🧐
Galaxy Server administration / Empathy 🧐
Galaxy Server administration / External Authentication ✍️ 🧐
Galaxy Server administration / Storage Management 🧐
Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
Galaxy Server administration / Reference Genomes in Galaxy 🧐
Galaxy Server administration / Docker and Galaxy 🧐
Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
Galaxy Server administration / User, Role, Group, Quota, and Authentication managment 🧐
Galaxy Server administration / Advanced customisation of a Galaxy instance 🧐
Galaxy Server administration / Ansible 🧐
Galaxy Server administration / Galaxy Troubleshooting 🧐
Galaxy Server administration / Galaxy from an administrator's point of view 🧐
Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
Galaxy Server administration / uWSGI 🧐
Galaxy Server administration / Server: Other 🧐
Galaxy Server administration / Connecting Galaxy to a compute cluster ✍️ 🧐
Galaxy Server administration / Galactic Database ✍️ 🧐
Introduction to Galaxy Analyses / Options for using Galaxy ✍️ 🧐
Introduction to Galaxy Analyses / Introduction to Galaxy ✍️ 🧐
Introduction to Galaxy Analyses / A Short Introduction to Galaxy ✍️ 🧐
Variant Analysis / Introduction to Variant analysis 🧐
Transcriptomics / Visualization of RNA-Seq results with CummeRbund 🧐
Transcriptomics / Introduction to Transcriptomics 🧐
Development in Galaxy / Galaxy Interactive Tours 🧐
Development in Galaxy / Visualizations: JavaScript Plugins 🧐
Development in Galaxy / Generic plugins 🧐
Development in Galaxy / Galaxy Code Architecture 🧐
Development in Galaxy / Prerequisites for building software/conda packages 🧐
Development in Galaxy / Scripting Galaxy using the API and BioBlend ✍️ 🧐
Development in Galaxy / Tool Shed: sharing Galaxy tools 🧐
Development in Galaxy / Tool development and integration into Galaxy ✍️ 🧐
Development in Galaxy / Galaxy Interactive Environments 🧐
Development in Galaxy / Tool Dependencies and Containers 🧐
Development in Galaxy / Tool Dependencies and Conda ✍️ 🧐
Development in Galaxy / Galaxy Webhooks 🧐
Introduction to Galaxy Analyses / Una breve introducción a Galaxy ✍️

FAQs

Events

2023 Galaxy Admin Training (Ghent) 🧑‍🏫

GitHub Activity

Issues Reported

101 Merged Pull Requests

See all of the github Pull Requests and github Commits by Nicola Soranzo.

Fix ELIXIR-UK typos
news

Spocathon-HDR-ELIXIR
Small fixes to the single-cell GO Enrichement tuto
single-cell

Spocathon-HDR-ELIXIR
Fix ``create-env`` Make command
template-and-tools

Spocathon-HDR-ELIXIR
Add affiliation and social ids for myself
template-and-tools
Fixes for the "Basics of machine learning" tutorial
statistics

Reviewed 203 PRs

We love our community reviewing each other's work!

Git-related improvements to Ansible-galaxy tutorial
admin
Update data library slides
admin
Break redirects to plain text slides
template-and-tools
Add ipynb faq
Update CoC to point to official Galaxy version

External Links

nsoranzo:matrix.org

https://mstdn.science/@nsoranzo

nicola-soranzo-7884125

0000-0003-3627-5340

Favourite Topics

Favourite Formats

Stats for materials contributed to by Nicola Soranzo