SIB Swiss Institute of Bioinformatics

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124 repositories

introduction-to-unix
Public
Introduction to Linux and the Bash shell
0•1•0•0•Updated Dec 23, 2024Dec 23, 2024
training-collection
Public
Collection of bioinformatics training materials
Python
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Other
•183•988•1•0•Updated Dec 22, 2024Dec 22, 2024
single-cell-python-training
Public
HTML
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Creative Commons Attribution 4.0 International
•0•1•0•0•Updated Dec 22, 2024Dec 22, 2024
spatial-transcriptomics-training
Public
R
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Creative Commons Attribution 4.0 International
•1•2•1•0•Updated Dec 22, 2024Dec 22, 2024
cancer-variants-training
Public
Lua
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Creative Commons Attribution 4.0 International
•2•2•0•0•Updated Dec 22, 2024Dec 22, 2024
sparql-llm
Public
🦜✨ Chat system and reusable components to improve LLMs capabilities when generating SPARQL queries
sparql sparql-query-builder expasy llm
Jupyter Notebook
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MIT License
•1•12•1•0•Updated Dec 19, 2024Dec 19, 2024
kgsteward
Public
Knwowledge Graph Steward - Command line tool to help manage RDF store (GraphDB)
Python
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GNU General Public License v3.0
•2•5•0•0•Updated Dec 19, 2024Dec 19, 2024
glittr
Public
A web application for finding and comparing bioinformatics training materials on GitHub and GitLab
PHP
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MIT License
•2•37•3•0•Updated Dec 19, 2024Dec 19, 2024
AWS-docker
Public
Set of commands to deploy docker containers on an AWS instance
teaching docker aws containers
Shell
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MIT License
•1•5•1•0•Updated Dec 19, 2024Dec 19, 2024
sparql-examples
Public
A set of SPARQL examples that are used in different SIB resources
HTML
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Other
•10•10•5•2•Updated Dec 18, 2024Dec 18, 2024
sparql-examples-utils
Public
A tool to maintain and test your SPARQL examples
quality sparql rdf
Java
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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
bioinformatics tutorial rna-seq course teaching single-cell
R
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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
rstats zenodo quarto
R
•1•1•1•0•Updated Dec 16, 2024Dec 16, 2024
ena-seqdata-training
Public
SIB course on interacting with ENA
Shell
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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
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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"
training docker dockerfile tutorial containers singularity teaching
HTML
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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
training tutorial course ngs teaching gatk variant-calling ngs-analysis
Shell
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Creative Commons Attribution 4.0 International
•9•25•2•0•Updated Dec 16, 2024Dec 16, 2024
NGS-longreads-training
Public
Shell
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Other
•3•9•9•0•Updated Dec 16, 2024Dec 16, 2024
NGS-introduction-training
Public
SIB course that introduces analysis of NGS data
training tutorial course teaching ngs-analysis
Shell
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Creative Commons Attribution 4.0 International
•12•15•4•0•Updated Dec 16, 2024Dec 16, 2024
glittr-stats
Public
General statistics of Glittr.org. Comes with the manuscript.
PostScript
•0•1•0•0•Updated Dec 15, 2024Dec 15, 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.
sparql sparql-query sparql-query-builder sparql-editor yasgui
TypeScript
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MIT License
•0•8•5•0•Updated Dec 12, 2024Dec 12, 2024
statistics-and-machine-learning-training
Public
Jupyter Notebook
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Creative Commons Attribution 4.0 International
•10•22•0•1•Updated Dec 9, 2024Dec 9, 2024
multiomics-data-analysis-and-integration-training
Public
HTML
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Other
•5•12•1•0•Updated Dec 2, 2024Dec 2, 2024
open-data-registry
Public
A registry of publicly available datasets on AWS
Python
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Apache License 2.0
•931•0•0•0•Updated Dec 1, 2024Dec 1, 2024
obelisk-docker
Public
Shell
•0•0•0•0•Updated Nov 29, 2024Nov 29, 2024
enrichment-analysis-training
Public
Course material for Enrichment analysis course by SIB
enrichment r enrichment-analysis gsea tutorial-course
Other
•8•8•5•0•Updated Nov 28, 2024Nov 28, 2024
fair-training-guide
Public
Creative Commons Attribution 4.0 International
•0•0•1•0•Updated Nov 27, 2024Nov 27, 2024
sendcrypt
Public
Modern and easy to use client to securely send encrypted sensitive data by SFTP. Linux, MacOS, and Windows.
encryption sftp-client openpgp sib sendcrypt
TypeScript
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MIT License
•0•1•0•0•Updated Nov 26, 2024Nov 26, 2024
dsSwissKnife
Public
R
•1•4•0•0•Updated Nov 26, 2024Nov 26, 2024
intermediate-python-training
Public
Jupyter Notebook
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Creative Commons Attribution 4.0 International
•27•63•4•0•Updated Nov 21, 2024Nov 21, 2024