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
- Microbiome / 16S Microbial Analysis with mothur (extended) 🧐
- Microbiome / Analyses of metagenomics data - The global picture 🧐
- Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐
- Using Galaxy and Managing your Data / Extracting Workflows from Histories 🧐
- 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 / Using dataset collections 🧐
- Using Galaxy and Managing your Data / Rule Based Uploader: Advanced 🧐
- Galaxy Server administration / Enable upload via FTP 🧐
- Galaxy Server administration / Galaxy Database schema 🧐
- Galaxy Server administration / Galaxy Installation with Ansible 📝 🧐
- Galaxy Server administration / Galaxy Interactive Tools 🧐
- Galaxy Server administration / Reference Data with CVMFS 🧐
- Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
- Galaxy Server administration / Data Libraries 🧐
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
- Galaxy Server administration / Ansible 🧐
- Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
- Galaxy Server administration / External Authentication ✍️ 🧐
- Galaxy Server administration / Distributed Object Storage 🧐
- Galaxy Server administration / Mapping Jobs to Destinations using TPV 🧐
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
- Galaxy Server administration / Reference Data with CVMFS without Ansible 🧐
- Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
- Galaxy Server administration / Automation with Jenkins 🧐
- Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
- Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
- Galaxy Server administration / Galaxy Monitoring with Reports 🧐
- Single Cell / Pre-processing of Single-Cell RNA Data 🧐
- Single Cell / Single-cell quality control with scater ✍️ 🧐
- Single Cell / Clustering 3K PBMCs with Scanpy 🧐
- Single Cell / Understanding Barcodes 🧐
- Teaching and Hosting Galaxy training / Set up a Galaxy for Training 🧐
- Teaching and Hosting Galaxy training / Galaxy Admin Training 🧐
- Teaching and Hosting Galaxy training / Running a workshop as instructor 🧐
- Ecology / RAD-Seq Reference-based data analysis 🧐
- Ecology / RAD-Seq to construct genetic maps 🧐
- Ecology / RAD-Seq de-novo data analysis 🧐
- Assembly / De Bruijn Graph Assembly 🧐
- Assembly / Making sense of a newly assembled genome 🧐
- Assembly / An Introduction to Genome Assembly 🧐
- Assembly / Unicycler Assembly 🧐
- Sequence analysis / Mapping 🧐
- Sequence analysis / Quality Control 🧐
- Statistics and machine learning / Interval-Wise Testing for omics data 🧐
- Epigenetics / Infinium Human Methylation BeadChip 🧐
- Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) 🧐
- Epigenetics / ATAC-Seq data analysis 🧐
- Epigenetics / Identification of the binding sites of the Estrogen receptor 🧐
- Epigenetics / DNA Methylation data analysis 🧐
- Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer 🧐
- Proteomics / Proteogenomics 2: Database Search 🧐
- Proteomics / Proteogenomics 3: Novel peptide analysis 🧐
- Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS 🧐
- Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method 🧐
- Proteomics / Protein FASTA Database Handling 🧐
- Proteomics / Secretome Prediction 🧐
- Proteomics / Metaproteomics tutorial 🧐
- Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
- Proteomics / Proteogenomics 1: Database Creation 🧐
- Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) 🧐
- Proteomics / Mass spectrometry imaging: Loading and exploring MSI data 🧐
- Proteomics / Peptide and Protein ID using OpenMS tools 🧐
- FAIR Data, Workflows, and Research / Metadata ✍️
- FAIR Data, Workflows, and Research / Data Registration ✍️
- FAIR Data, Workflows, and Research / Access ✍️
- FAIR Data, Workflows, and Research / FAIR and its Origins ✍️
- FAIR Data, Workflows, and Research / Persistent Identifiers ✍️
- Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours 🧐
- Contributing to the Galaxy Training Material / Including a new topic 🧐
- Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line 🧐
- Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
- Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
- Contributing to the Galaxy Training Material / Running the GTN website locally using the command line 🧐
- Contributing to the Galaxy Training Material / Adding auto-generated video to your slides 🧐
- Contributing to the Galaxy Training Material / Contributing with GitHub via its interface 🧐
- Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
- Contributing to the Galaxy Training Material / Generating PDF artefacts of the website 🧐
- Transcriptomics / Differential abundance testing of small RNAs 🧐
- Transcriptomics / 3: RNA-seq genes to pathways 🧐
- Transcriptomics / De novo transcriptome reconstruction with RNA-Seq 🧐
- Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot 🧐
- Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection 🧐
- Transcriptomics / 1: RNA-Seq reads to counts 🧐
- Transcriptomics / 2: RNA-seq counts to genes 🧐
- Transcriptomics / Visualization of RNA-Seq results with CummeRbund 🧐
- Transcriptomics / Reference-based RNAseq data analysis (long) 🧐
- Transcriptomics / Network analysis with Heinz 🧐
- Transcriptomics / Visualization of RNA-Seq results with heatmap2 🧐
- Variant Analysis / Calling very rare variants 🧐
- Variant Analysis / Calling variants in non-diploid systems 🧐
- Variant Analysis / Calling variants in diploid systems ✍️ 🧐
- Variant Analysis / Mapping and molecular identification of phenotype-causing mutations 🧐
- 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 / Microbial Variant Calling 🧐
- Genome Annotation / Genome annotation with Maker 🧐
- Genome Annotation / Genome annotation with Prokka 🧐
- Genome Annotation / Genome Annotation 🧐
- Development in Galaxy / Scripting Galaxy using the API and BioBlend ✍️ 🧐
- Development in Galaxy / Data source integration 🧐
- Development in Galaxy / JavaScript plugins 🧐
- Development in Galaxy / Generic plugins 🧐
- Development in Galaxy / Galaxy Webhooks 🧐
- Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐
- Introduction to Galaxy Analyses / A short introduction to Galaxy ✍️ 🧐
- Introduction to Galaxy Analyses / From peaks to genes ✍️ 🧐
- Introduction to Galaxy Analyses / IGV Introduction 🧐
- Introduction to Galaxy Analyses / NGS data logistics 🧐
- Introduction to Galaxy Analyses / Galaxy Basics for genomics ✍️ 🧐
- Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
Slides
- Development in Galaxy / Galaxy from a developer point of view 🧐
- Microbiome / Introduction to Microbiome Analysis 🧐
- Using Galaxy and Managing your Data / Getting data into Galaxy 🧐
- Galaxy Server administration / Terraform 🧐
- Galaxy Server administration / Controlling Galaxy with systemd or Supervisor 🧐
- Galaxy Server administration / uWSGI 🧐
- Galaxy Server administration / Galaxy Installation with Ansible 🧐
- Galaxy Server administration / Gearing towards production 🧐
- Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration 🧐
- Galaxy Server administration / Galaxy Interactive Tools 🧐
- Galaxy Server administration / Reference Data with CVMFS 🧐
- Galaxy Server administration / Storage Management 🧐
- Galaxy Server administration / Galaxy on the Cloud 🧐
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
- Galaxy Server administration / Ansible 🧐
- Galaxy Server administration / Reference Genomes in Galaxy 🧐
- Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
- Galaxy Server administration / External Authentication ✍️ 🧐
- Galaxy Server administration / Empathy 🧐
- Galaxy Server administration / Advanced customisation of a Galaxy instance 🧐
- Galaxy Server administration / Storage Management 🧐
- Galaxy Server administration / Galactic Database ✍️ 🧐
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
- Galaxy Server administration / User, Role, Group, Quota, and Authentication managment 🧐
- Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
- Galaxy Server administration / Galaxy Troubleshooting 🧐
- Galaxy Server administration / Galaxy from an administrator's point of view 🧐
- Galaxy Server administration / Connecting Galaxy to a compute cluster ✍️ 🧐
- Galaxy Server administration / Docker and Galaxy 🧐
- Galaxy Server administration / Server: Other 🧐
- Assembly / De Bruijn Graph Assembly 🧐
- Assembly / An Introduction to Genome Assembly 🧐
- Assembly / Unicycler Assembly 🧐
- Sequence analysis / Mapping 🧐
- Sequence analysis / Quality Control 🧐
- Epigenetics / Introduction to DNA Methylation data analysis 🧐
- Epigenetics / Introduction to ChIP-Seq data analysis 🧐
- Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 🧐
- 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 🧐
- Transcriptomics / Visualization of RNA-Seq results with CummeRbund 🧐
- Transcriptomics / Introduction to Transcriptomics 🧐
- Variant Analysis / Introduction to Variant analysis 🧐
- Genome Annotation / Genome annotation with Prokka 🧐
- Development in Galaxy / Scripting Galaxy using the API and BioBlend ✍️ 🧐
- Development in Galaxy / Galaxy Interactive Tours 🧐
- Development in Galaxy / Tool Shed: sharing Galaxy tools 🧐
- Development in Galaxy / Visualizations: JavaScript Plugins 🧐
- Development in Galaxy / Generic plugins 🧐
- Development in Galaxy / Tool Dependencies and Containers 🧐
- Development in Galaxy / Tool Dependencies and Conda ✍️ 🧐
- Development in Galaxy / Galaxy Interactive Environments 🧐
- Development in Galaxy / Tool development and integration into Galaxy ✍️ 🧐
- Development in Galaxy / Galaxy Webhooks 🧐
- Development in Galaxy / Prerequisites for building software/conda packages 🧐
- Development in Galaxy / Galaxy Code Architecture 🧐
- Introduction to Galaxy Analyses / A Short Introduction to Galaxy ✍️ 🧐
- Introduction to Galaxy Analyses / Options for using Galaxy ✍️ 🧐
- Introduction to Galaxy Analyses / Introduction to Galaxy ✍️ 🧐
- Introduction to Galaxy Analyses / Una breve introducción a Galaxy ✍️
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
- Créer un nouvel history
- Creating a new history
- Opening the workflow editor
- Extracting a workflow from your history
Events
GitHub Activity
github Issues Reported
98 Merged Pull Requests
See all of the github Pull Requests and github Commits by Nicola Soranzo.
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Add affiliation and social ids for myself
template-and-tools -
Fixes for the "Basics of machine learning" tutorial
statistics
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Small fixes to Intro short tutorial
introductionfaqs
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Update tool integration slides
devtemplate-and-tools
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Git-related improvements to Ansible-galaxy tutorial
admin
Reviewed 203 PRs
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