Repositories list

• training-collection

  Public
  Collection of bioinformatics training materials

  Python

  •

  Other

  •184•993•1•0•Updated Jan 12, 2025Jan 12, 2025

• single-cell-python-training

  Public
  HTML

  •

  Creative Commons Attribution 4.0 International

  •0•3•0•0•Updated Jan 12, 2025Jan 12, 2025

• spatial-transcriptomics-training

  Public
  R

  •

  Creative Commons Attribution 4.0 International

  •1•2•1•0•Updated Jan 12, 2025Jan 12, 2025

• glittr-stats

  Public
  General statistics of Glittr.org. Comes with the manuscript.

  PostScript

  •0•1•0•0•Updated Jan 12, 2025Jan 12, 2025

• cancer-variants-training

  Public
  Lua

  •

  Creative Commons Attribution 4.0 International

  •2•3•0•0•Updated Jan 12, 2025Jan 12, 2025

• fair-training-guide

  Public
  Creative Commons Attribution 4.0 International

  •0•0•1•0•Updated Jan 10, 2025Jan 10, 2025

• kgsteward

  Public
  Knowledge Graph Steward - Command line tool to help manage RDF store

  Python

  •

  GNU General Public License v3.0

  •2•5•0•0•Updated Jan 10, 2025Jan 10, 2025

• Introduction-to-statistics-with-R

  Public
  Other

  •2•4•1•3•Updated Jan 10, 2025Jan 10, 2025

• AWS-docker

  Public
  Set of commands to deploy docker containers on an AWS instance

  teachingdockeraws+ 1containers

  Shell

  •

  MIT License

  •1•5•0•0•Updated Jan 9, 2025Jan 9, 2025

• enrichment-analysis-training

  Public
  Course material for Enrichment analysis course by SIB

  enrichmentrenrichment-analysis+ 2gseatutorial-course

  Other

  •8•8•5•0•Updated Jan 7, 2025Jan 7, 2025

• intermediate-python-training

  Public
  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •27•63•4•0•Updated Jan 6, 2025Jan 6, 2025

• first-steps-with-python-training

  Public
  repository of the 3-day course "First steps with Python in Life Sciences" from SIB-training

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •17•56•6•0•Updated Jan 6, 2025Jan 6, 2025

• sparql-llm

  Public
  🦜✨ Chat system and reusable components to improve LLMs capabilities when generating SPARQL queries

  sparqlsparql-query-builderexpasy+ 1llm

  Jupyter Notebook

  •

  MIT License

  •1•13•1•0•Updated Jan 6, 2025Jan 6, 2025

• introduction-to-unix

  Public
  Introduction to Linux and the Bash shell

  0•1•0•0•Updated Dec 23, 2024Dec 23, 2024

• glittr

  Public
  A web application for finding and comparing bioinformatics training materials on GitHub and GitLab

  PHP

  •

  MIT License

  •2•37•3•0•Updated Dec 19, 2024Dec 19, 2024

• sparql-examples

  Public
  A set of SPARQL examples that are used in different SIB resources

  HTML

  •

  Other

  •10•10•5•2•Updated Dec 18, 2024Dec 18, 2024

• sparql-examples-utils

  Public
  A tool to maintain and test your SPARQL examples

  qualitysparqlrdf

  Java

  •

  Other

  •10•4•14•2•Updated Dec 18, 2024Dec 18, 2024

• single-cell-training

  Public
  SIB course on single cell transcriptomics by mostly using the Seurat pipeline

  bioinformaticstutorialrna-seq+ 3courseteachingsingle-cell

  R

  •

  Creative Commons Attribution 4.0 International

  •36•78•2•0•Updated Dec 16, 2024Dec 16, 2024

• reproducible-analysis-training

  Public
  SIB course on FAIR analysis with Quarto, GitHub and Zenodo

  rstatszenodoquarto

  R

  •1•1•1•0•Updated Dec 16, 2024Dec 16, 2024

• ena-seqdata-training

  Public
  SIB course on interacting with ENA

  Shell

  •

  Other

  •0•0•1•0•Updated Dec 16, 2024Dec 16, 2024

• containers-snakemake-training

  Public
  Course website "Introduction to Containers and Snakemake for Reproducible Research"

  Dockerfile

  •

  Creative Commons Attribution 4.0 International

  •14•5•0•0•Updated Dec 16, 2024Dec 16, 2024

• containers-introduction-training

  Public
  Course website "Docker and Singularity for reproducible research: getting started with containers"

  trainingdockerdockerfile+ 4tutorialcontainerssingularityteaching

  HTML

  •

  Creative Commons Attribution 4.0 International

  •14•29•1•0•Updated Dec 16, 2024Dec 16, 2024

• NGS-variants-training

  Public
  GitHub for the SIB courses NGS - Genome variant analysis

  trainingtutorialcourse+ 5ngsteachinggatkvariant-callingngs-analysis

  Shell

  •

  Creative Commons Attribution 4.0 International

  •9•25•2•0•Updated Dec 16, 2024Dec 16, 2024

• NGS-longreads-training

  Public
  Shell

  •

  Other

  •3•9•9•0•Updated Dec 16, 2024Dec 16, 2024

• NGS-introduction-training

  Public
  SIB course that introduces analysis of NGS data

  trainingtutorialcourse+ 2teachingngs-analysis

  Shell

  •

  Creative Commons Attribution 4.0 International

  •12•15•4•0•Updated Dec 16, 2024Dec 16, 2024

• sparql-editor

  Public
  💫 A standard web component to deploy a user-friendly SPARQL query editor for one or more endpoints. Built on the popular YASGUI editor, it provides context-aware autocomplete for classes and predicates based on the content of the endpoints.

  sparqlsparql-querysparql-query-builder+ 2sparql-editoryasgui

  TypeScript

  •

  MIT License

  •0•8•6•0•Updated Dec 12, 2024Dec 12, 2024

• statistics-and-machine-learning-training

  Public
  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •11•23•0•1•Updated Dec 9, 2024Dec 9, 2024

• multiomics-data-analysis-and-integration-training

  Public
  HTML

  •

  Other

  •6•18•1•0•Updated Dec 2, 2024Dec 2, 2024

• open-data-registry

  Public
  A registry of publicly available datasets on AWS

  Python

  •

  Apache License 2.0

  •936•0•0•0•Updated Dec 1, 2024Dec 1, 2024

• obelisk-docker

  Public
  Shell

  •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024