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88 repositories

scverse.github.io
Public
scverse.org website
SCSS
•11•4•9•4•Updated Aug 15, 2026Aug 15, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•84•38•6•15•Updated Aug 15, 2026Aug 15, 2026
gget
Public
🧬 gget enables efficient querying of genomic reference databases
rna-seq genomics reference
rna-seq genomics reference databases ensembl proteomics blast transcriptomics uniprot ncbi
Python
•
BSD 2-Clause "Simplified" License
•92•1.2k•25•18•Updated Aug 15, 2026Aug 15, 2026
rustar-aligner
Public
A rust implementation of STAR
Rust
•
MIT License
•7•70•31•30•Updated Aug 14, 2026Aug 14, 2026
spatialdata-plot-tutorials
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•2•Updated Aug 14, 2026Aug 14, 2026
squidpy
Public
Spatial Single Cell Analysis in Python
data-visualization spatial-analysis image-analysis
data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy
Python
•
BSD 3-Clause "New" or "Revised" License
•118•588•77•19•Updated Aug 14, 2026Aug 14, 2026
spatialdata
Public
An open and interoperable data framework for spatial omics data
spatial spatial-analysis spatial-data
spatial spatial-analysis spatial-data scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•92•383•264•16•Updated Aug 14, 2026Aug 14, 2026
decoupler
Public
Python package to perform enrichment analysis from omics data.
python data-science bioinformatics
python data-science bioinformatics enrichment numba transcriptomics single-cell enrichment-analysis spatial-transcriptomics scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•37•288•3•2•Updated Aug 14, 2026Aug 14, 2026
scanpy
Public
Single-cell analysis in Python. Scales to >100M cells.
python data-science machine-learning
python data-science machine-learning bioinformatics transcriptomics visualize-data scanpy anndata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•762•2.5k•440•83•Updated Aug 14, 2026Aug 14, 2026
Muon.jl
Public
Muon for Julia
julia muon omics
julia muon omics single-cell multi-omics anndata mudata scverse
Julia
•
BSD 3-Clause "New" or "Revised" License
•6•29•1•0•Updated Aug 14, 2026Aug 14, 2026
mudata
Public
Multimodal Data (.h5mu) implementation for Python
genomics muon data-analysis
genomics muon data-analysis multi-omics anndata multimodal-omics-analysis mudata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•23•130•8•0•Updated Aug 14, 2026Aug 14, 2026
muon
Public
muon is a multimodal omics Python framework
muon scrna-seq multi-omics
muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata
Python
•
BSD 3-Clause "New" or "Revised" License
•37•279•36•9•Updated Aug 14, 2026Aug 14, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•4•15•16•4•Updated Aug 14, 2026Aug 14, 2026
governance
Public
Governance docs for scverse
governance scverse
governance scverse
BSD 3-Clause "New" or "Revised" License
•0•9•11•0•Updated Aug 14, 2026Aug 14, 2026
stats
Public
scverse statistics
TypeScript
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MIT License
•0•4•7•0•Updated Aug 14, 2026Aug 14, 2026
rapids-singlecell
Public
rapids-singlecell: GPU-accelerated framework for scRNA analysis
bioinformatics gpu single-cell
bioinformatics gpu single-cell anndata scverse
Python
•
MIT License
•48•391•10•10•Updated Aug 14, 2026Aug 14, 2026
spatialdata-tutorials
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•26•67•8•1•Updated Aug 14, 2026Aug 14, 2026
anndata
Public
Annotated data.
data-science machine-learning bioinformatics
data-science machine-learning bioinformatics transcriptomics scanpy anndata scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•206•764•185•84•Updated Aug 14, 2026Aug 14, 2026
anndataR
Public
AnnData interoperability in R
interoperability anndata h5ad
interoperability anndata h5ad
R
•
Other
•22•192•37•8•Updated Aug 14, 2026Aug 14, 2026
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•21•82•18•3•Updated Aug 13, 2026Aug 13, 2026
pertpy
Public
Single-cell perturbation analysis
python bioinformatics computational-biology
python bioinformatics computational-biology drug-discovery scrna-seq crispr single-cell differential-expression perturbation anndata
Python
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MIT License
•63•337•12•4•Updated Aug 13, 2026Aug 13, 2026
benchmark
Public
Code for running benchmarks
Rust
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GNU General Public License v3.0
•0•4•7•1•Updated Aug 12, 2026Aug 12, 2026
scvi-tutorials
Public
Notebooks used in scvi-tools tutorials
tutorial scvi-tools scverse
tutorial scvi-tools scverse
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•35•65•0•4•Updated Aug 12, 2026Aug 12, 2026
scvi-tools
Public
Deep probabilistic analysis of single-cell and spatial omics data
deep-learning scrna-seq variational-autoencoder
deep-learning scrna-seq variational-autoencoder variational-bayes single-cell-genomics single-cell-rna-seq deep-generative-model cite-seq human-cell-atlas scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•472•1.7k•11•13•Updated Aug 12, 2026Aug 12, 2026
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•62•100•68•8•Updated Aug 11, 2026Aug 11, 2026
cookiecutter-scverse-instance
Public
Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the templat…
Python
•
BSD 3-Clause "New" or "Revised" License
•6•5•0•4•Updated Aug 11, 2026Aug 11, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•18•89•22•3•Updated Aug 11, 2026Aug 11, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•2•9•1•0•Updated Aug 11, 2026Aug 11, 2026
cookiecutter-scverse-presentation
Public
Introduction to our template
0•2•0•0•Updated Aug 11, 2026Aug 11, 2026
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•1•1•0•Updated Aug 11, 2026Aug 11, 2026

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88 repositories