Nicola Soranzo
Affiliations
Earlham Institute
ELIXIR EuropeContributions
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
- Sequence analysis / Quality Control π§
- Sequence analysis / Mapping π§
- Transcriptomics / 1: RNA-Seq reads to counts π§
- Transcriptomics / De novo transcriptome reconstruction with RNA-Seq π§
- Transcriptomics / 2: RNA-seq counts to genes π§
- Transcriptomics / Visualization of RNA-Seq results with CummeRbund π§
- Transcriptomics / 3: RNA-seq genes to pathways π§
- Transcriptomics / Network analysis with Heinz π§
- Transcriptomics / Reference-based RNAseq data analysis (long) π§
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot π§
- Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection π§
- Transcriptomics / Differential abundance testing of small RNAs π§
- Transcriptomics / Reference-based RNA-Seq data analysis βοΈ π§
- Transcriptomics / Visualization of RNA-Seq results with heatmap2 π§
- Statistics and machine learning / Interval-Wise Testing for omics data π§
- Contributing to the Galaxy Training Material / Creating content in Markdown π§
- Contributing to the Galaxy Training Material / Updating diffs in admin training π§
- Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials π§
- Contributing to the Galaxy Training Material / Creating a new tutorial π§
- Contributing to the Galaxy Training Material / Contributing with GitHub via its interface π§
- Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours π§
- Contributing to the Galaxy Training Material / Contributing to the Galaxy Training Network with GitHub π§
- Contributing to the Galaxy Training Material / Generating PDF artefacts of the website π§
- Contributing to the Galaxy Training Material / Including a new topic π§
- Contributing to the Galaxy Training Material / Adding auto-generated video to your slides π§
- Epigenetics / ATAC-Seq data analysis π§
- Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer π§
- Epigenetics / Identification of the binding sites of the Estrogen receptor π§
- Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) π§
- Epigenetics / Infinium Human Methylation BeadChip π§
- Epigenetics / DNA Methylation data analysis π§
- Genome Annotation / Genome Annotation π§
- Genome Annotation / Genome annotation with Maker π§
- Genome Annotation / Genome annotation with Prokka π§
- Introduction to Galaxy Analyses / From peaks to genes βοΈ π§
- Introduction to Galaxy Analyses / NGS data logistics π§
- Introduction to Galaxy Analyses / IGV Introduction π§
- Introduction to Galaxy Analyses / Galaxy Basics for genomics βοΈ π§
- Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy π§
- Introduction to Galaxy Analyses / A short introduction to Galaxy βοΈ π§
- Introduction to Galaxy Analyses / Galaxy Basics for everyone π§
- FAIR Data, Workflows, and Research / Data Registration βοΈ
- FAIR Data, Workflows, and Research / FAIR and its Origins βοΈ
- FAIR Data, Workflows, and Research / Metadata βοΈ
- FAIR Data, Workflows, and Research / Persistent Identifiers βοΈ
- FAIR Data, Workflows, and Research / Access βοΈ
- Assembly / Making sense of a newly assembled genome π§
- Assembly / De Bruijn Graph Assembly π§
- Assembly / Unicycler Assembly π§
- Assembly / An Introduction to Genome Assembly π§
- Development in Galaxy / Data source integration π§
- Development in Galaxy / Scripting Galaxy using the API and BioBlend βοΈ π§
- Development in Galaxy / Galaxy Webhooks π§
- Development in Galaxy / JavaScript plugins π§
- Development in Galaxy / Generic plugins π§
- Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) π§
- Proteomics / Proteogenomics 3: Novel peptide analysis π§
- Proteomics / Mass spectrometry imaging: Loading and exploring MSI data π§
- Proteomics / Peptide and Protein ID using OpenMS tools π§
- Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS π§
- Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method π§
- Proteomics / Protein FASTA Database Handling π§
- Proteomics / Secretome Prediction π§
- Proteomics / Proteogenomics 2: Database Search π§
- Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker π§
- Proteomics / Metaproteomics tutorial π§
- Proteomics / Proteogenomics 1: Database Creation π§
- Using Galaxy and Managing your Data / Rule Based Uploader: Advanced π§
- Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy π§
- Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows π§
- Using Galaxy and Managing your Data / Using dataset collections π§
- Using Galaxy and Managing your Data / Understanding Galaxy history system π§
- Using Galaxy and Managing your Data / Extracting Workflows from Histories π§
- Teaching and Hosting Galaxy training / Set up a Galaxy for Training π§
- Teaching and Hosting Galaxy training / Galaxy Admin Training π§
- Teaching and Hosting Galaxy training / Running a workshop as instructor π§
- Galaxy Server administration / Galaxy Interactive Tools π§
- Galaxy Server administration / Reference Data with CVMFS without Ansible π§
- Galaxy Server administration / Enable upload via FTP π§
- Galaxy Server administration / Galaxy Monitoring with gxadmin π§
- Galaxy Server administration / External Authentication βοΈ π§
- Galaxy Server administration / Galaxy Monitoring with Reports π§
- Galaxy Server administration / Galaxy Installation with Ansible π π§
- Galaxy Server administration / Mapping Jobs to Destinations using TPV π§
- Galaxy Server administration / Automation with Jenkins π§
- Galaxy Server administration / Reference Data with CVMFS π§
- Galaxy Server administration / Distributed Object Storage π§
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana π§
- Galaxy Server administration / Galaxy Database schema π§
- Galaxy Server administration / Use Apptainer containers for running Galaxy jobs π§
- Galaxy Server administration / Data Libraries π§
- Galaxy Server administration / Galaxy Tool Management with Ephemeris βοΈ π§
- Galaxy Server administration / Connecting Galaxy to a compute cluster π§
- Galaxy Server administration / Training Infrastructure as a Service (TIaaS) π§
- Galaxy Server administration / Ansible π§
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar π§
- Microbiome / Analyses of metagenomics data - The global picture π§
- Microbiome / 16S Microbial Analysis with mothur (extended) π§
- Variant Analysis / Calling variants in non-diploid systems π§
- Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis π§
- Variant Analysis / Calling variants in diploid systems βοΈ π§
- Variant Analysis / Mapping and molecular identification of phenotype-causing mutations π§
- Variant Analysis / Calling very rare variants π§
- Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease π§
- Variant Analysis / Microbial Variant Calling π§
- Single Cell / Understanding Barcodes π§
- Single Cell / Single-cell quality control with scater βοΈ π§
- Single Cell / Pre-processing of Single-Cell RNA Data π§
- Single Cell / Clustering 3K PBMCs with Scanpy π§
- Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data π
- Ecology / RAD-Seq to construct genetic maps π§
- Ecology / RAD-Seq de-novo data analysis π§
- Ecology / RAD-Seq Reference-based data analysis π§
Slides
- Development in Galaxy / Galaxy from a developer point of view π§
- Sequence analysis / Quality Control π§
- Sequence analysis / Mapping π§
- Transcriptomics / Visualization of RNA-Seq results with CummeRbund π§
- Transcriptomics / Introduction to Transcriptomics π§
- Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material π§
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line π§
- Contributing to the Galaxy Training Material / Creating Slides π§
- Epigenetics / Introduction to DNA Methylation data analysis π§
- Epigenetics / Introduction to ChIP-Seq data analysis π§
- Genome Annotation / Genome annotation with Prokka π§
- Introduction to Galaxy Analyses / Introduction to Galaxy βοΈ π§
- Introduction to Galaxy Analyses / Options for using Galaxy βοΈ π§
- Introduction to Galaxy Analyses / A Short Introduction to Galaxy βοΈ π§
- Assembly / De Bruijn Graph Assembly π§
- Assembly / Unicycler Assembly π§
- Assembly / An Introduction to Genome Assembly π§
- Development in Galaxy / Tool Shed: sharing Galaxy tools π§
- Development in Galaxy / Prerequisites for building software/conda packages π§
- Development in Galaxy / Galaxy Code Architecture π§
- Development in Galaxy / Scripting Galaxy using the API and BioBlend βοΈ π§
- Development in Galaxy / Galaxy Webhooks π§
- Development in Galaxy / Visualizations: JavaScript Plugins π§
- Development in Galaxy / Tool Dependencies and Containers π§
- Development in Galaxy / Generic plugins π§
- Development in Galaxy / Galaxy Interactive Environments π§
- Development in Galaxy / Galaxy Interactive Tours π§
- Development in Galaxy / Tool development and integration into Galaxy βοΈ π§
- Development in Galaxy / Tool Dependencies and Conda βοΈ π§
- Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling π§
- Using Galaxy and Managing your Data / Getting data into Galaxy π§
- Galaxy Server administration / Galaxy Interactive Tools π§
- Galaxy Server administration / User, Role, Group, Quota, and Authentication managment π§
- Galaxy Server administration / uWSGI π§
- Galaxy Server administration / Galaxy on the Cloud π§
- Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration π§
- Galaxy Server administration / Gearing towards production π§
- Galaxy Server administration / Reference Genomes in Galaxy π§
- Galaxy Server administration / Galactic Database βοΈ π§
- Galaxy Server administration / Galaxy Monitoring with gxadmin π§
- Galaxy Server administration / Advanced customisation of a Galaxy instance π§
- Galaxy Server administration / Controlling Galaxy with systemd or Supervisor π§
- Galaxy Server administration / External Authentication βοΈ π§
- Galaxy Server administration / Server: Other π§
- Galaxy Server administration / Galaxy from an administrator's point of view π§
- Galaxy Server administration / Galaxy Installation with Ansible π§
- Galaxy Server administration / Reference Data with CVMFS π§
- Galaxy Server administration / Empathy π§
- Galaxy Server administration / Terraform π§
- Galaxy Server administration / Storage Management π§
- Galaxy Server administration / Galaxy Troubleshooting π§
- Galaxy Server administration / Docker and Galaxy π§
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana π§
- Galaxy Server administration / Storage Management π§
- Galaxy Server administration / Galaxy Tool Management with Ephemeris βοΈ π§
- Galaxy Server administration / Connecting Galaxy to a compute cluster βοΈ π§
- Galaxy Server administration / Ansible π§
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar π§
- Microbiome / Introduction to Microbiome Analysis π§
- Variant Analysis / Introduction to Variant analysis π§
- Introduction to Galaxy Analyses / Una breve introducciΓ³n a Galaxy βοΈ
FAQs
- How do I know what I can do with a role? What variables are available?
- Contributing a Jupyter Notebook to the GTN
- Changing the datatype
- Detecting the datatype (file format)
- Importing data from a data library
- Importing data from remote files
- Renaming a dataset
- Creating a new history
- CrΓ©er un nouvel history
- Opening the workflow editor
- Extracting a workflow from your history
Events
- 2023 Galaxy Admin Training (Ghent) π§βπ«
GitHub Activity
github Issues Reported
101 Merged Pull Requests
See all of the github Pull Requests and github Commits by Nicola Soranzo.
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Fix ELIXIR-UK typos
newsSpocathon-HDR-ELIXIR -
Small fixes to the single-cell GO Enrichement tuto
single-cellSpocathon-HDR-ELIXIR
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Fix ``create-env`` Make command
template-and-toolsSpocathon-HDR-ELIXIR
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Add affiliation and social ids for myself
template-and-tools
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Fixes for the "Basics of machine learning" tutorial
statistics
Reviewed 204 PRs
We love our community reviewing each other's work!
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Added admin survey as a news post
news -
Git-related improvements to Ansible-galaxy tutorial
admin
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Update data library slides
admin
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Break redirects to plain text slides
template-and-tools -
Add ipynb faq
News
Survey about a week-long Galaxy Admin Training in Europe
External Links
Favourite Topics
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