scverse repositories

93 repositories

rapids-singlecell
Public
rapids-singlecell: GPU-accelerated framework for scRNA analysis
bioinformatics gpu single-cell
bioinformatics gpu single-cell anndata scverse
Python
•
MIT License
•51•394•11•10•Updated Sep 2, 2026Sep 2, 2026
cell-painting-io
Public
Experimental! A collection of scripts & utilities to get Cell Painting datasets into scverse data structures.
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Sep 2, 2026Sep 2, 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
•471•1.7k•13•13•Updated Sep 2, 2026Sep 2, 2026
benchmark
Public
Code for running benchmarks
Rust
•
GNU General Public License v3.0
•0•4•7•2•Updated Sep 2, 2026Sep 2, 2026
scverse.github.io
Public
scverse.org website
SCSS
•11•4•9•4•Updated Sep 2, 2026Sep 2, 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
•23•133•9•0•Updated Sep 2, 2026Sep 2, 2026
sp-ops
Public
Prototype schema and APIs for OPS support in SpatialData
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Sep 2, 2026Sep 2, 2026
annbatch
Public
Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse
Python
•
MIT License
•6•68•23•12•Updated Sep 2, 2026Sep 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
•208•768•185•85•Updated Sep 2, 2026Sep 2, 2026
2026_08_hackathon_cellpainting
Public
Jupyter Notebook
•1•5•0•1•Updated Sep 2, 2026Sep 2, 2026
scirpy
Public
A scanpy extension to analyse single-cell TCR and BCR data.
airr scverse
airr scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•49•265•35•11•Updated Sep 2, 2026Sep 2, 2026
sc-proteomics2026
Public
HTML
•1•4•0•0•Updated Sep 2, 2026Sep 2, 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
•35•65•0•4•Updated Sep 2, 2026Sep 2, 2026
pertpy
Public
Single-cell perturbation analysis
python bioinformatics computational-biology
python bioinformatics computational-biology drug-discovery scrna-seq crispr single-cell differential-expression perturbation anndata
Python
•
MIT License
•64•337•9•4•Updated Sep 2, 2026Sep 2, 2026
acumen
Public
Python
•
MIT License
•1•7•1•0•Updated Sep 1, 2026Sep 1, 2026
liana-py
Public
LIANA+: an all-in-one framework for cell-cell communication
python spatial single-cell
python spatial single-cell single-cell-rna-seq ligand-receptor cell-cell-communication spatialomics
Python
•
BSD 3-Clause "New" or "Revised" License
•37•313•16•2•Updated Sep 1, 2026Sep 1, 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
•767•2.6k•439•89•Updated Sep 1, 2026Sep 1, 2026
spatialdata
Public
An open and interoperable data framework for spatial omics data
spatial spatial-analysis spatial-data
spatial spatial-analysis spatial-data scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•92•387•263•17•Updated Sep 1, 2026Sep 1, 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
•24•88•69•4•Updated Sep 1, 2026Sep 1, 2026
pandas-uuid
Public
Pandas ExtensionArray / ExtensionDType for UUID
Python
•
Mozilla Public License 2.0
•0•2•6•0•Updated Sep 1, 2026Sep 1, 2026
ecosystem-packages
Public
Registry for scverse ecosystem packages
Python
•
BSD 3-Clause "New" or "Revised" License
•88•39•6•16•Updated Sep 1, 2026Sep 1, 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 Sep 1, 2026Sep 1, 2026
cookiecutter-scverse
Public
Cookiecutter template for scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•17•88•22•3•Updated Sep 1, 2026Sep 1, 2026
scvi-colab
Public
Lightweight helper to install scvi-tools in Google Colab
googlecolab scvi-tools scverse
googlecolab scvi-tools scverse
Python
•
BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Sep 1, 2026Sep 1, 2026
fast-array-utils
Public
Fast array utilities
Python
•
Mozilla Public License 2.0
•4•15•16•4•Updated Sep 1, 2026Sep 1, 2026
repo-health
Public
Automated checks for security and consistency on scverse.org github repositories
Python
•
Mozilla Public License 2.0
•0•1•3•4•Updated Sep 1, 2026Sep 1, 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
•94•1.2k•25•18•Updated Sep 1, 2026Sep 1, 2026
spatialdata-io
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•62•101•68•8•Updated Sep 1, 2026Sep 1, 2026
session-info2
Public
Python
•
Mozilla Public License 2.0
•2•9•1•0•Updated Aug 31, 2026Aug 31, 2026
muon
Public
muon is a multimodal omics Python framework
muon scrna-seq multi-omics
muon scrna-seq multi-omics multimodal-data cite-seq scanpy scatac-seq anndata multimodal-omics-analysis mudata
Python
•
BSD 3-Clause "New" or "Revised" License
•37•278•10•1•Updated Aug 31, 2026Aug 31, 2026

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93 repositories

rapids-singlecell

cell-painting-io

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benchmark

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mudata

sp-ops

annbatch

anndata

2026_08_hackathon_cellpainting

scirpy

sc-proteomics2026

scvi-tutorials

pertpy

acumen

liana-py

scanpy

spatialdata

napari-spatialdata

pandas-uuid

ecosystem-packages

cookiecutter-scverse-instance

cookiecutter-scverse

scvi-colab

fast-array-utils

repo-health

gget

spatialdata-io

session-info2

muon

Repositories list

93 repositories