Nicola Soranzo
Affiliations
BioFAIR
Earlham Institute
ELIXIR Europe
ELIXIR-STEERSContributions
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
- Variant Analysis / Calling variants in diploid systems βοΈ π§
- Variant Analysis / Calling very rare variants π§
- Variant Analysis / Microbial Variant Calling π§
- Variant Analysis / Mapping and molecular identification of phenotype-causing mutations π§
- Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis π§
- Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease π§
- Variant Analysis / Calling variants in non-diploid systems π§
- Using Galaxy and Managing your Data / Rule Based Uploader: Advanced π§
- Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows π§
- Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy π§
- Using Galaxy and Managing your Data / Understanding Galaxy history system π§
- Using Galaxy and Managing your Data / Extracting Workflows from Histories π§
- Using Galaxy and Managing your Data / Using dataset collections π§
- FAIR Data, Workflows, and Research / Access βοΈ
- FAIR Data, Workflows, and Research / FAIR and its Origins βοΈ
- FAIR Data, Workflows, and Research / Persistent Identifiers βοΈ
- FAIR Data, Workflows, and Research / Data Registration βοΈ
- FAIR Data, Workflows, and Research / Metadata βοΈ
- Ecology / RAD-Seq to construct genetic maps π§
- Ecology / RAD-Seq Reference-based data analysis π§
- Ecology / RAD-Seq de-novo data analysis π§
- Microbiome / 16S Microbial Analysis with mothur (extended) π§
- Microbiome / Analyses of metagenomics data - The global picture π§
- Development in Galaxy / JavaScript plugins π§
- Development in Galaxy / Generic plugins π§
- Development in Galaxy / Galaxy Webhooks π§
- Development in Galaxy / Scripting Galaxy using the API and BioBlend βοΈ π§
- Development in Galaxy / Data source integration π§
- Teaching and Hosting Galaxy training / Running a workshop as an instructor π§
- Teaching and Hosting Galaxy training / Set up a Galaxy for Training π§
- Teaching and Hosting Galaxy training / Galaxy Admin Training π§
- Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy π§
- Introduction to Galaxy Analyses / Galaxy Basics for genomics βοΈ π§
- Introduction to Galaxy Analyses / From peaks to genes βοΈ π§
- Introduction to Galaxy Analyses / A short introduction to Galaxy βοΈ π§
- Introduction to Galaxy Analyses / Galaxy Basics for everyone π§
- Introduction to Galaxy Analyses / NGS data logistics π§
- Introduction to Galaxy Analyses / IGV Introduction π§
- Sequence analysis / Mapping π§
- Sequence analysis / Quality Control π§
- Statistics and machine learning / Interval-Wise Testing for omics data π§
- Galaxy Server administration / Training Infrastructure as a Service (TIaaS) π§
- Galaxy Server administration / External Authentication βοΈ π§
- Galaxy Server administration / Mapping Jobs to Destinations using TPV π§
- Galaxy Server administration / Distributed Object Storage π§
- Galaxy Server administration / Monitoring Galaxy and Pulsar with Sentry π§
- Galaxy Server administration / Performant Uploads with TUS π§
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana π§
- Galaxy Server administration / Ansible π§
- Galaxy Server administration / Galaxy Installation with Ansible π π§
- Galaxy Server administration / Galaxy Monitoring with gxadmin π§
- Galaxy Server administration / Galaxy Tool Management with Ephemeris βοΈ π§
- Galaxy Server administration / Connecting Galaxy to a compute cluster π§
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar π§
- Galaxy Server administration / Galaxy Monitoring with Reports π§
- Galaxy Server administration / Galaxy Database schema π§
- Galaxy Server administration / Enable upload via FTP π§
- Galaxy Server administration / Reference Data with CVMFS π§
- Galaxy Server administration / Reference Data with CVMFS without Ansible π§
- Galaxy Server administration / Galaxy Interactive Tools π§
- Galaxy Server administration / Automation with Jenkins π§
- Galaxy Server administration / Use Apptainer containers for running Galaxy jobs π§
- Galaxy Server administration / Data Libraries π§
- Genome Annotation / Genome annotation with Prokka π§
- Genome Annotation / Genome Annotation π§
- Genome Annotation / Genome annotation with Maker π§
- Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker π§
- Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) π§
- Proteomics / Proteogenomics 1: Database Creation π§
- Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method π§
- Proteomics / Peptide and Protein ID using OpenMS tools π§
- Proteomics / Metaproteomics tutorial π§
- Proteomics / Mass spectrometry imaging: Loading and exploring MSI data π§
- Proteomics / Proteogenomics 2: Database Search π§
- Proteomics / Secretome Prediction π§
- Proteomics / Protein FASTA Database Handling π§
- Proteomics / Proteogenomics 3: Novel peptide analysis π§
- Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS π§
- Assembly / Making sense of a newly assembled genome π§
- Assembly / Unicycler Assembly π§
- Assembly / An Introduction to Genome Assembly π§
- Assembly / De Bruijn Graph Assembly π§
- Transcriptomics / Visualization of RNA-Seq results with CummeRbund π§
- Transcriptomics / Network analysis with Heinz π§
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot π§
- Transcriptomics / Differential abundance testing of small RNAs π§
- Transcriptomics / 2: RNA-seq counts to genes π§
- Transcriptomics / 3: RNA-seq genes to pathways π§
- Transcriptomics / Reference-based RNA-Seq data analysis βοΈ π§
- Transcriptomics / Visualization of RNA-Seq results with heatmap2 π§
- Transcriptomics / Reference-based RNAseq data analysis (long) π§
- Transcriptomics / 1: RNA-Seq reads to counts π§
- Transcriptomics / De novo transcriptome reconstruction with RNA-Seq π§
- Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection π§
- Single Cell / Understanding Barcodes π§
- Single Cell / Single-cell quality control with scater βοΈ π§
- Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data π
- Single Cell / Pre-processing of Single-Cell RNA Data π§
- Single Cell / Clustering 3K PBMCs with Scanpy π§
- Epigenetics / Identification of the binding sites of the Estrogen receptor π§
- Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer π§
- Epigenetics / DNA Methylation data analysis π§
- Epigenetics / ATAC-Seq data analysis π§
- Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) π§
- Epigenetics / Infinium Human Methylation BeadChip π§
- Contributing to the Galaxy Training Material / Contributing with GitHub via its interface π§
- Contributing to the Galaxy Training Material / Contributing to the Galaxy Training Network with GitHub π§
- Contributing to the Galaxy Training Material / Updating diffs in admin training π§
- Contributing to the Galaxy Training Material / Creating content in Markdown π§
- Contributing to the Galaxy Training Material / Adding auto-generated video to your slides π§
- Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 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 / Creating a new tutorial π§
- Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours π§
- Introduction to Galaxy Analyses / Von Peaks zu Genen βοΈ
- Transcriptomics / Referenzbasierte RNA-Seq-Datenanalyse βοΈ
- Introduction to Galaxy Analyses / De picos a genes βοΈ
- Transcriptomics / AnΓ‘lisis de datos RNA-Seq basados en referencias βοΈ
- Introduction to Galaxy Analyses / Dai picchi ai geni βοΈ
- Transcriptomics / Analisi dei dati RNA-Seq basata su riferimenti βοΈ
Slides
- Development in Galaxy / Galaxy from a developer point of view π§
- Variant Analysis / Introduction to Variant analysis π§
- Using Galaxy and Managing your Data / Getting data into Galaxy π§
- Microbiome / Introduction to Microbiome Analysis π§
- Development in Galaxy / Visualizations: JavaScript Plugins π§
- Development in Galaxy / Tool Dependencies and Conda βοΈ π§
- Development in Galaxy / Generic plugins π§
- Development in Galaxy / Prerequisites for building software/conda packages π§
- Development in Galaxy / Galaxy Webhooks π§
- Development in Galaxy / Tool Dependencies and Containers π§
- Development in Galaxy / Scripting Galaxy using the API and BioBlend βοΈ π§
- Development in Galaxy / Galaxy Interactive Tours π§
- Development in Galaxy / Galaxy Interactive Environments π§
- Development in Galaxy / Tool development and integration into Galaxy βοΈ π§
- Development in Galaxy / Tool Shed: sharing Galaxy tools π§
- Introduction to Galaxy Analyses / Introduction to Galaxy βοΈ π§
- Introduction to Galaxy Analyses / A Short Introduction to Galaxy βοΈ π§
- Introduction to Galaxy Analyses / Options for using Galaxy βοΈ π§
- Sequence analysis / Mapping π§
- Sequence analysis / Quality Control π§
- Galaxy Server administration / External Authentication βοΈ π§
- Galaxy Server administration / Reference Genomes in Galaxy π§
- Galaxy Server administration / Storage Management π§
- Galaxy Server administration / Terraform π§
- Galaxy Server administration / Docker and Galaxy π§
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana π§
- Galaxy Server administration / Ansible π§
- Galaxy Server administration / Empathy 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 / Galaxy Monitoring with gxadmin 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 / Server Maintenance: Cleanup, Backup, and Restoration π§
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar π§
- Galaxy Server administration / uWSGI π§
- Galaxy Server administration / Gearing towards production π§
- Galaxy Server administration / Galaxy Troubleshooting π§
- Galaxy Server administration / Galactic Database βοΈ π§
- Galaxy Server administration / Reference Data with CVMFS π§
- Galaxy Server administration / User, Role, Group, Quota, and Authentication managment π§
- Galaxy Server administration / Galaxy Interactive Tools π§
- Galaxy Server administration / Controlling Galaxy with systemd or Supervisor π§
- Galaxy Server administration / Advanced customisation of a Galaxy instance π§
- Galaxy Server administration / Galaxy on the Cloud π§
- Galaxy Server administration / Storage Management π§
- Genome Annotation / Genome annotation with Prokka π§
- Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling π§
- Assembly / Unicycler Assembly π§
- Assembly / An Introduction to Genome Assembly π§
- Assembly / De Bruijn Graph Assembly π§
- Transcriptomics / Visualization of RNA-Seq results with CummeRbund π§
- Transcriptomics / Introduction to Transcriptomics π§
- Epigenetics / Introduction to DNA Methylation data analysis π§
- Epigenetics / Introduction to ChIP-Seq data analysis π§
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line π§
- Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material π§
- Contributing to the Galaxy Training Material / Creating Slides 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
- Modifica del tipo di dato βοΈ
- Changing the datatype
- Γndern des Datentyps βοΈ
- Detecting the datatype (file format)
- Importare i dati da una libreria di dati βοΈ
- Importing data from a data library
- Importar datos de una biblioteca de datos βοΈ
- Importieren von Daten aus einer Datenbibliothek βοΈ
- Importing data from repositories
- Rinominare un set di dati βοΈ
- Renaming a dataset
- Cambiar el nombre de un conjunto de datos βοΈ
- Umbenennen eines Datensatzes βοΈ
- Creare una nuova cronologia βοΈ
- Creating a new history
- CrΓ©er un nouvel history
- Para la creaciΓ³n de un historial nuevo βοΈ
- Erstellen eines neuen Verlaufs βοΈ
- Opening the workflow editor
- Extracting a workflow from your history
Events
- 2023 Galaxy Admin Training (Ghent) π§βπ«
GitHub Activity
github Issues Reported
103 Merged Pull Requests
See all of the github Pull Requests and github Commits by Nicola Soranzo.
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Add ELIXIR-STEERS grant
template-and-tools -
Enable dependabot version updates for GitHub actions
template-and-tools
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Fix ELIXIR-UK typos
newsSpocathon-HDR-ELIXIR
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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
Reviewed 212 PRs
We love our community reviewing each other's work!
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Add setuptools pulsar requirement and drop amqp pin
admin -
Fix following logs
admin
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[GAT] Fix success check of tusd upload
admin
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Bump aws-actions/configure-aws-credentials from 1 to 5
template-and-toolsdependenciesgithub_actions -
Bump peaceiris/actions-gh-pages from 3 to 4
template-and-toolsdependenciesgithub_actions
News
Survey about a week-long Galaxy Admin Training in Europe
External Links
Favourite Topics
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