All

80 repositories

ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•74•36•7•8•Updated May 1, 2026May 1, 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
•57•443•20•4•Updated May 1, 2026May 1, 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
•447•1.6k•14•11•Updated Apr 30, 2026Apr 30, 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
•741•2.4k•480•82•Updated Apr 30, 2026Apr 30, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•3•14•15•3•Updated Apr 30, 2026Apr 30, 2026
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•58•93•67•7•Updated Apr 30, 2026Apr 30, 2026
integration-testing
Public
A repo for integration testing core packages against upstream core packages
MIT License
•0•1•2•0•Updated Apr 30, 2026Apr 30, 2026
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•16•20•12•6•Updated Apr 30, 2026Apr 30, 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
•43•360•13•10•Updated Apr 30, 2026Apr 30, 2026
scverse.github.io
Public
scverse.org website
SCSS
•10•4•15•3•Updated Apr 30, 2026Apr 30, 2026
rapids_singlecell-notebooks
Public
Jupyter Notebook
•
MIT License
•3•12•0•0•Updated Apr 30, 2026Apr 30, 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
•190•735•191•70•Updated Apr 30, 2026Apr 30, 2026
pertpy
Public
Single-cell perturbation analysis
single-cell perturbation scverse
single-cell perturbation scverse
Python
•
MIT License
•56•309•34•5•Updated Apr 30, 2026Apr 30, 2026
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
•
BSD 3-Clause "New" or "Revised" License
•47•250•38•6•Updated Apr 29, 2026Apr 29, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•3•55•26•12•Updated Apr 29, 2026Apr 29, 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 Apr 29, 2026Apr 29, 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
•22•120•10•2•Updated Apr 29, 2026Apr 29, 2026
anndataR
Public
AnnData interoperability in R
interoperability anndata h5ad
interoperability anndata h5ad
R
•
Other
•19•170•31•8•Updated Apr 28, 2026Apr 28, 2026
scverse-misc
Public
Miscellaneous utility code used by scverse packages
Python
•
BSD 3-Clause "New" or "Revised" License
•0•4•5•0•Updated Apr 28, 2026Apr 28, 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 Apr 28, 2026Apr 28, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•17•90•24•6•Updated Apr 28, 2026Apr 28, 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 Apr 28, 2026Apr 28, 2026
cookiecutter-scverse-presentation
Public
Introduction to our template
0•2•0•0•Updated Apr 28, 2026Apr 28, 2026
zulip-bots
Public
Repository for zulip bots for scverse.zulipchat.com
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Apr 28, 2026Apr 28, 2026
anndata-plot
Public
Python
•
MIT License
•3•8•1•4•Updated Apr 28, 2026Apr 28, 2026
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•1•1•0•Updated Apr 28, 2026Apr 28, 2026
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•122•235•15•1•Updated Apr 28, 2026Apr 28, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•2•7•1•0•Updated Apr 28, 2026Apr 28, 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 Apr 28, 2026Apr 28, 2026
simple-scvi
Public
Simple scVI implementation
Python
•
BSD 3-Clause "New" or "Revised" License
•5•12•0•3•Updated Apr 27, 2026Apr 27, 2026

ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

scverse

All

All

80 repositories

ecosystem-packages

cellrank

scvi-tools

scanpy

fast-array-utils

spatialdata-io

integration-testing

scverse-tutorials

rapids-singlecell

scverse.github.io

rapids_singlecell-notebooks

anndata

pertpy

scirpy

annbatch

scvi-tutorials

mudata

anndataR

scverse-misc

2026_04_hackathon_padua

cookiecutter-scverse

cookiecutter-scverse-instance

cookiecutter-scverse-presentation

zulip-bots

anndata-plot

prelude-runner

scanpy-tutorials

session-info2

scvi-colab

simple-scvi

All

All

Repositories list

80 repositories