All

80 repositories

antibody-based-spatial-proteomics-guide
Public
Guide for common steps in analyzing antiboy-based spatial proteomics data, part of the scverse proteomics consortium.
BSD 3-Clause "New" or "Revised" License
•0•3•0•0•Updated Apr 22, 2026Apr 22, 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
•189•732•189•73•Updated Apr 22, 2026Apr 22, 2026
scverse.github.io
Public
scverse.org website
SCSS
•9•3•15•1•Updated Apr 22, 2026Apr 22, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•74•36•7•8•Updated Apr 22, 2026Apr 22, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•3•53•26•10•Updated Apr 22, 2026Apr 22, 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•16•13•Updated Apr 22, 2026Apr 22, 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
•738•2.4k•479•85•Updated Apr 22, 2026Apr 22, 2026
pertpy
Public
Single-cell perturbation analysis
single-cell perturbation scverse
single-cell perturbation scverse
Python
•
MIT License
•56•308•32•5•Updated Apr 22, 2026Apr 22, 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
•35•266•1•1•Updated Apr 21, 2026Apr 21, 2026
PyDESeq2
Public
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
python bioinformatics rna-seq
python bioinformatics rna-seq transcriptomics differential-expression
Python
•
MIT License
•83•747•39•10•Updated Apr 21, 2026Apr 21, 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•356•14•8•Updated Apr 21, 2026Apr 21, 2026
rapids_singlecell-notebooks
Public
Jupyter Notebook
•
MIT License
•3•12•0•0•Updated Apr 21, 2026Apr 21, 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
•113•563•69•30•Updated Apr 21, 2026Apr 21, 2026
scverse-misc
Public
Miscellaneous utility code used by scverse packages
Python
•
BSD 3-Clause "New" or "Revised" License
•0•4•4•1•Updated Apr 21, 2026Apr 21, 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•117•10•3•Updated Apr 21, 2026Apr 21, 2026
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•20•78•23•4•Updated Apr 20, 2026Apr 20, 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 20, 2026Apr 20, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•2•7•1•0•Updated Apr 20, 2026Apr 20, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•17•90•24•5•Updated Apr 20, 2026Apr 20, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•3•14•15•4•Updated Apr 20, 2026Apr 20, 2026
cookiecutter-scverse-presentation
Public
Introduction to our template
0•2•0•0•Updated Apr 20, 2026Apr 20, 2026
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•1•1•0•Updated Apr 20, 2026Apr 20, 2026
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•16•20•12•5•Updated Apr 20, 2026Apr 20, 2026
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•122•235•15•1•Updated Apr 20, 2026Apr 20, 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 20, 2026Apr 20, 2026
anndata-plot
Public
Python
•
MIT License
•3•8•1•4•Updated Apr 20, 2026Apr 20, 2026
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•13•60•13•2•Updated Apr 20, 2026Apr 20, 2026
formulaic-contrasts
Public
Build contrasts for models defined with formulaic
Python
•
BSD 3-Clause "New" or "Revised" License
•2•12•2•2•Updated Apr 20, 2026Apr 20, 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 Apr 20, 2026Apr 20, 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•84•69•4•Updated Apr 20, 2026Apr 20, 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

antibody-based-spatial-proteomics-guide

anndata

scverse.github.io

ecosystem-packages

annbatch

scvi-tools

scanpy

pertpy

decoupler

PyDESeq2

rapids-singlecell

rapids_singlecell-notebooks

squidpy

scverse-misc

mudata

spatialdata-plot

cookiecutter-scverse-instance

session-info2

cookiecutter-scverse

fast-array-utils

cookiecutter-scverse-presentation

prelude-runner

scverse-tutorials

scanpy-tutorials

zulip-bots

anndata-plot

pytometry

formulaic-contrasts

plotting_api

napari-spatialdata

All

All

Repositories list

80 repositories