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78 repositories

spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•18•77•26•3•Updated Apr 4, 2026Apr 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
•444•1.6k•15•11•Updated Apr 3, 2026Apr 3, 2026
anndataR
Public
AnnData interoperability in R
interoperability anndata h5ad
interoperability anndata h5ad
R
•
Other
•16•167•30•6•Updated Apr 2, 2026Apr 2, 2026
pertpy
Public
Single-cell perturbation analysis
single-cell perturbation scverse
single-cell perturbation scverse
Python
•
MIT License
•54•301•29•4•Updated Apr 2, 2026Apr 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•3•Updated Apr 2, 2026Apr 2, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•17•90•24•5•Updated Apr 2, 2026Apr 2, 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
•110•559•65•24•Updated Apr 2, 2026Apr 2, 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
•185•729•188•70•Updated Apr 2, 2026Apr 2, 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
•22•82•68•3•Updated Apr 1, 2026Apr 1, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•3•29•23•8•Updated Apr 1, 2026Apr 1, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•73•36•8•8•Updated Apr 1, 2026Apr 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•437•20•2•Updated Apr 1, 2026Apr 1, 2026
202603_hackathon_proteomics
Public
Jupyter Notebook
•5•7•3•2•Updated Mar 31, 2026Mar 31, 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
•44•349•14•9•Updated Mar 31, 2026Mar 31, 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
•21•111•10•5•Updated Mar 31, 2026Mar 31, 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
•729•2.4k•482•82•Updated Mar 31, 2026Mar 31, 2026
scverse.github.io
Public
scverse.org website
SCSS
•9•3•15•1•Updated Mar 31, 2026Mar 31, 2026
cookiecutter-scverse-presentation
Public
Introduction to our template
0•2•0•0•Updated Mar 31, 2026Mar 31, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•2•14•14•4•Updated Mar 31, 2026Mar 31, 2026
zulip-bots
Public
Repository for zulip bots for scverse.zulipchat.com
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Mar 31, 2026Mar 31, 2026
anndata-plot
Public
Python
•
MIT License
•3•8•1•4•Updated Mar 31, 2026Mar 31, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•1•7•1•0•Updated Mar 31, 2026Mar 31, 2026
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•16•20•12•5•Updated Mar 31, 2026Mar 31, 2026
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•1•1•0•Updated Mar 31, 2026Mar 31, 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 Mar 31, 2026Mar 31, 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
•32•64•1•4•Updated Mar 31, 2026Mar 31, 2026
scverse-misc
Public
Miscellaneous utility code used by scverse packages
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Mar 30, 2026Mar 30, 2026
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•13•60•13•2•Updated Mar 30, 2026Mar 30, 2026
plotting_api
Public
Experimenting with a simplified plotting API for scanpy/scirpy
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•2•3•2•Updated Mar 30, 2026Mar 30, 2026
spatialdata-notebooks
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•25•65•9•1•Updated Mar 30, 2026Mar 30, 2026

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scverse

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78 repositories

spatialdata-plot

scvi-tools

anndataR

pertpy

cookiecutter-scverse-instance

cookiecutter-scverse

squidpy

anndata

napari-spatialdata

annbatch

ecosystem-packages

cellrank

202603_hackathon_proteomics

rapids-singlecell

mudata

scanpy

scverse.github.io

cookiecutter-scverse-presentation

fast-array-utils

zulip-bots

anndata-plot

session-info2

scverse-tutorials

prelude-runner

scvi-colab

scvi-tutorials

scverse-misc

pytometry

plotting_api

spatialdata-notebooks

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Repositories list

78 repositories