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83 repositories

scverse.github.io
Public
scverse.org website
SCSS
•10•4•16•2•Updated Jun 7, 2026Jun 7, 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
•116•575•75•29•Updated Jun 7, 2026Jun 7, 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
Python
•
BSD 3-Clause "New" or "Revised" License
•36•269•1•2•Updated Jun 7, 2026Jun 7, 2026
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•21•82•28•2•Updated Jun 7, 2026Jun 7, 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
•46•374•13•7•Updated Jun 6, 2026Jun 6, 2026
rustar-aligner
Public
A rust implementation of STAR
Rust
•
MIT License
•3•47•4•5•Updated Jun 5, 2026Jun 5, 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
•749•2.5k•484•91•Updated Jun 5, 2026Jun 5, 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
•196•749•193•73•Updated Jun 5, 2026Jun 5, 2026
cellrank
Public
CellRank: dynamics from multi-view single-cell data
data-science machine-learning bioinformatics
data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning single-cell-genomics single-cell-rna-seq cell-fate-transitions
Python
•
BSD 3-Clause "New" or "Revised" License
•56•452•3•1•Updated Jun 5, 2026Jun 5, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•3•62•27•14•Updated Jun 5, 2026Jun 5, 2026
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•25•66•9•1•Updated Jun 5, 2026Jun 5, 2026
2026_04_hackathon_padua
Public
Repository to organize and share code for the scverse Padua Hackathon, April 2026
Jupyter Notebook
•0•3•37•0•Updated Jun 4, 2026Jun 4, 2026
anndataR
Public
AnnData interoperability in R
interoperability anndata h5ad
interoperability anndata h5ad
R
•
Other
•20•183•33•7•Updated Jun 4, 2026Jun 4, 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
•458•1.6k•16•16•Updated Jun 3, 2026Jun 3, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•77•37•7•13•Updated Jun 3, 2026Jun 3, 2026
pertpy
Public
Single-cell perturbation analysis
single-cell perturbation scverse
single-cell perturbation scverse
Python
•
MIT License
•59•324•15•5•Updated Jun 3, 2026Jun 3, 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•122•9•3•Updated Jun 2, 2026Jun 2, 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 Jun 1, 2026Jun 1, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•18•90•25•6•Updated Jun 1, 2026Jun 1, 2026
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•125•237•15•1•Updated Jun 1, 2026Jun 1, 2026
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•16•21•12•5•Updated Jun 1, 2026Jun 1, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•2•9•1•0•Updated Jun 1, 2026Jun 1, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•3•14•15•3•Updated Jun 1, 2026Jun 1, 2026
cookiecutter-scverse-presentation
Public
Introduction to our template
0•2•0•0•Updated Jun 1, 2026Jun 1, 2026
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•1•1•0•Updated Jun 1, 2026Jun 1, 2026
zulip-bots
Public
Repository for zulip bots for scverse.zulipchat.com
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jun 1, 2026Jun 1, 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
•33•64•1•3•Updated Jun 1, 2026Jun 1, 2026
scvi-colab
Public
Lightweight helper to install scvi-tools in Google Colab
Python
•
BSD 3-Clause "New" or "Revised" License
•1•2•1•0•Updated Jun 1, 2026Jun 1, 2026
scverse-misc
Public
Miscellaneous utility code used by scverse packages
Python
•
BSD 3-Clause "New" or "Revised" License
•0•4•7•1•Updated Jun 1, 2026Jun 1, 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•28•1•0•Updated Jun 1, 2026Jun 1, 2026

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scverse

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83 repositories

scverse.github.io

squidpy

decoupler

spatialdata-plot

rapids-singlecell

rustar-aligner

scanpy

anndata

cellrank

annbatch

spatialdata-notebooks

2026_04_hackathon_padua

anndataR

scvi-tools

ecosystem-packages

pertpy

mudata

cookiecutter-scverse-instance

cookiecutter-scverse

scanpy-tutorials

scverse-tutorials

session-info2

fast-array-utils

cookiecutter-scverse-presentation

prelude-runner

zulip-bots

scvi-tutorials

scvi-colab

scverse-misc

Muon.jl

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Repositories list

83 repositories