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

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

Slides

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