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README.md

Welcome to scverse®!

scverse® is a community that develops and maintains foundational tools for single-cell omics data analysis in primarily Python.

Here's how to get started:

📚 See available packages on the website.
👩‍💻 Check out the learning page.
Come and say hi on our zulip!
👩 Get to know the people behind scverse, get involved!
🌈 Please abide by our community code of conduct

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scanpy scanpy Public

Single-cell analysis in Python. Scales to >100M cells.

Python 2.6k 808
anndata anndata Public

Annotated data.

Python 785 223
scvi-tools scvi-tools Public

Deep probabilistic analysis of single-cell and spatial omics data

Python 1.7k 483
squidpy squidpy Public

Spatial Single Cell Analysis in Python

Python 614 128
rapids-singlecell rapids-singlecell Public

rapids-singlecell: GPU-accelerated framework for scRNA analysis

Python 410 55
pertpy pertpy Public

Single-cell perturbation analysis

Python 360 71

Repositories

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Showing 10 of 107 repositories

scanpy Public
Single-cell analysis in Python. Scales to >100M cells.

scverse/scanpy's past year of commit activity

Python 2,615 BSD-3-Clause 808 431 (3 issues need help) 102 Updated Nov 12, 2026
spatialdata-spec Public
Specification for the SpatialData format

scverse/spatialdata-spec's past year of commit activity

2 0 2 7 Updated Nov 12, 2026
scverse.github.io Public
scverse.org website

scverse/scverse.github.io's past year of commit activity

SCSS 4 MPL-2.0 11 4 1 Updated Nov 12, 2026
anndataR Public
AnnData interoperability in R

scverse/anndataR's past year of commit activity

R 201 25 45 7 Updated Nov 12, 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 template.

scverse/cookiecutter-scverse-instance's past year of commit activity

Python 5 BSD-3-Clause 6 0 7 Updated Nov 12, 2026
cookiecutter-scverse Public
Cookiecutter template for scverse

scverse/cookiecutter-scverse's past year of commit activity

Python 91 BSD-3-Clause 17 27 5 Updated Nov 12, 2026
anndata Public
Annotated data.

scverse/anndata's past year of commit activity

Python 785 BSD-3-Clause 223 192 (4 issues need help) 93 Updated Nov 12, 2026
cupy-stubs Public
Type stubs for CuPy

scverse/cupy-stubs's past year of commit activity

Python 4 MPL-2.0 0 2 3 Updated Nov 12, 2026
mantispy Public
Analysis framework for morphological profiling data

scverse/mantispy's past year of commit activity

Python 18 BSD-3-Clause 1 49 7 Updated Nov 12, 2026
zarr-kvikio Public

scverse/zarr-kvikio's past year of commit activity

Python 2 MIT 0 0 2 Updated Nov 12, 2026