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85 repositories

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
•756•2.5k•477•91•Updated Jul 15, 2026Jul 15, 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 Jul 15, 2026Jul 15, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•18•89•21•4•Updated Jul 15, 2026Jul 15, 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•1•Updated Jul 15, 2026Jul 15, 2026
scverse-misc
Public
Miscellaneous utility code used by scverse packages
Python
•
BSD 3-Clause "New" or "Revised" License
•1•5•5•1•Updated Jul 15, 2026Jul 15, 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•126•9•2•Updated Jul 15, 2026Jul 15, 2026
benchmark
Public
Code for running benchmarks
Rust
•
GNU General Public License v3.0
•0•4•7•1•Updated Jul 15, 2026Jul 15, 2026
scverse.github.io
Public
scverse.org website
SCSS
•11•4•13•4•Updated Jul 15, 2026Jul 15, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•81•37•7•16•Updated Jul 15, 2026Jul 15, 2026
gget
Public
🧬 gget enables efficient querying of genomic reference databases
rna-seq genomics reference
rna-seq genomics reference databases ensembl proteomics blast transcriptomics uniprot ncbi
Python
•
BSD 2-Clause "Simplified" License
•91•1.2k•25•18•Updated Jul 15, 2026Jul 15, 2026
anndata-rs
Public
Rust
•15•50•9•4•Updated Jul 15, 2026Jul 15, 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
•48•382•12•9•Updated Jul 14, 2026Jul 14, 2026
spatialdata
Public
An open and interoperable data framework for spatial omics data
Python
•
BSD 3-Clause "New" or "Revised" License
•88•381•261•11•Updated Jul 14, 2026Jul 14, 2026
integration-testing
Public
A repo for integration testing core packages against upstream core packages
MIT License
•0•1•1•0•Updated Jul 14, 2026Jul 14, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•4•15•16•4•Updated Jul 14, 2026Jul 14, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•2•9•1•1•Updated Jul 14, 2026Jul 14, 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
•201•759•187•74•Updated Jul 14, 2026Jul 14, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•6•67•21•13•Updated Jul 14, 2026Jul 14, 2026
cookiecutter-scverse-presentation
Public
Introduction to our template
0•2•0•0•Updated Jul 14, 2026Jul 14, 2026
scverse-tutorials
Public
Tutorials for learning scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•16•22•12•5•Updated Jul 14, 2026Jul 14, 2026
prelude-runner
Public
Jupyter notebook runner that executes preludes before each cell
Python
•
Apache License 2.0
•0•1•1•0•Updated Jul 14, 2026Jul 14, 2026
scanpy-tutorials
Public
Scanpy Tutorials.
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•124•240•15•1•Updated Jul 14, 2026Jul 14, 2026
zulip-bots
Public
Repository for zulip bots for scverse.zulipchat.com
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jul 14, 2026Jul 14, 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
•467•1.7k•13•11•Updated Jul 14, 2026Jul 14, 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 Jul 14, 2026Jul 14, 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
•34•64•1•4•Updated Jul 14, 2026Jul 14, 2026
pertpy
Public
Single-cell perturbation analysis
single-cell perturbation scverse
single-cell perturbation scverse
Python
•
MIT License
•61•337•19•3•Updated Jul 13, 2026Jul 13, 2026
simple-scvi
Public
Simple scVI implementation
Python
•
BSD 3-Clause "New" or "Revised" License
•5•13•0•3•Updated Jul 13, 2026Jul 13, 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
•117•583•71•25•Updated Jul 13, 2026Jul 13, 2026
pytometry
Public
Flow & mass cytometry analytics.
Python
•
Apache License 2.0
•15•60•13•3•Updated Jul 13, 2026Jul 13, 2026

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scverse

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85 repositories

scanpy

cookiecutter-scverse-instance

cookiecutter-scverse

Muon.jl

scverse-misc

mudata

benchmark

scverse.github.io

ecosystem-packages

gget

anndata-rs

rapids-singlecell

spatialdata

integration-testing

fast-array-utils

session-info2

anndata

annbatch

cookiecutter-scverse-presentation

scverse-tutorials

prelude-runner

scanpy-tutorials

zulip-bots

scvi-tools

scvi-colab

scvi-tutorials

pertpy

simple-scvi

squidpy

pytometry

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Repositories list

85 repositories