All

81 repositories

scverse-backends
Public
Python
•
MIT License
•0•1•0•0•Updated May 5, 2026May 5, 2026
anndataR
Public
AnnData interoperability in R
interoperability anndata h5ad
interoperability anndata h5ad
R
•
Other
•19•172•31•9•Updated May 5, 2026May 5, 2026
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•87•365•257•16•Updated May 5, 2026May 5, 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
•449•1.6k•14•14•Updated May 5, 2026May 5, 2026
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•25•66•9•0•Updated May 5, 2026May 5, 2026
napari-spatialdata
Public
Interactive visualization of spatial omics data
visualization spatial-analysis napari-plugin
visualization spatial-analysis napari-plugin napari spatial-omics
Python
•
BSD 3-Clause "New" or "Revised" License
•23•85•69•3•Updated May 5, 2026May 5, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•3•14•15•3•Updated May 5, 2026May 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
•741•2.4k•481•84•Updated May 5, 2026May 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
•191•737•192•72•Updated May 5, 2026May 5, 2026
scverse.github.io
Public
scverse.org website
SCSS
•10•4•15•2•Updated May 5, 2026May 5, 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 May 5, 2026May 5, 2026
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•58•94•66•3•Updated May 5, 2026May 5, 2026
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
Python
•
BSD 3-Clause "New" or "Revised" License
•47•251•34•5•Updated May 5, 2026May 5, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•3•56•26•10•Updated May 4, 2026May 4, 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 May 4, 2026May 4, 2026
cookiecutter-scverse-presentation
Public
Introduction to our template
0•2•0•0•Updated May 4, 2026May 4, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•17•90•24•6•Updated May 4, 2026May 4, 2026
anndata-plot
Public
Python
•
MIT License
•3•8•1•4•Updated May 4, 2026May 4, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•2•7•1•0•Updated May 4, 2026May 4, 2026
zulip-bots
Public
Repository for zulip bots for scverse.zulipchat.com
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated May 4, 2026May 4, 2026
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•16•20•12•5•Updated May 4, 2026May 4, 2026
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•122•235•15•2•Updated May 4, 2026May 4, 2026
scverse-misc
Public
Miscellaneous utility code used by scverse packages
Python
•
BSD 3-Clause "New" or "Revised" License
•0•4•5•0•Updated May 4, 2026May 4, 2026
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•13•60•13•2•Updated May 4, 2026May 4, 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 4, 2026May 4, 2026
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•20•80•57•5•Updated May 4, 2026May 4, 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
•114•567•72•30•Updated May 4, 2026May 4, 2026
pandas-uuid
Public
Pandas ExtensionArray / ExtensionDType for UUID
Python
•
Mozilla Public License 2.0
•0•2•6•2•Updated May 4, 2026May 4, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•74•37•7•9•Updated May 4, 2026May 4, 2026
pertpy
Public
Single-cell perturbation analysis
single-cell perturbation scverse
single-cell perturbation scverse
Python
•
MIT License
•57•309•31•6•Updated May 4, 2026May 4, 2026

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scverse

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All

81 repositories

scverse-backends

anndataR

spatialdata

scvi-tools

spatialdata-notebooks

napari-spatialdata

fast-array-utils

scanpy

anndata

scverse.github.io

mudata

spatialdata-io

scirpy

annbatch

cookiecutter-scverse-instance

cookiecutter-scverse-presentation

cookiecutter-scverse

anndata-plot

session-info2

zulip-bots

scverse-tutorials

scanpy-tutorials

scverse-misc

pytometry

cellrank

spatialdata-plot

squidpy

pandas-uuid

ecosystem-packages

pertpy

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Repositories list

81 repositories