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scverse

Foundational tools for omics data in the life sciences
README.md

Welcome to scverse®!

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:

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  1. scanpy scanpy Public

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

    Python 2.6k 796

  2. anndata anndata Public

    Annotated data.

    Python 779 220

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 479

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 606 124

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 401 53

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 347 68

Repositories

Showing 10 of 97 repositories
  • 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 5 Updated Oct 13, 2026
  • muon Public

    muon is a multimodal omics Python framework

    scverse/muon's past year of commit activity
    Python 279 BSD-3-Clause 37 9 2 Updated Oct 13, 2026
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse's past year of commit activity
    Python 91 BSD-3-Clause 18 24 4 Updated Oct 13, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 401 MIT 53 12 14 Updated Oct 13, 2026
  • cellrank Public

    CellRank: dynamics from multi-view single-cell data

    scverse/cellrank's past year of commit activity
    Python 458 BSD-3-Clause 58 2 3 Updated Oct 13, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 86 MIT 9 39 28 Updated Oct 13, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 606 BSD-3-Clause 124 78 (1 issue needs help) 24 Updated Oct 13, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,585 BSD-3-Clause 796 449 (3 issues need help) 106 Updated Oct 13, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 27 10 2 Updated Oct 13, 2026
  • Muon.jl Public

    Muon for Julia

    scverse/Muon.jl's past year of commit activity
    Julia 30 BSD-3-Clause 6 1 (1 issue needs help) 0 Updated Oct 13, 2026
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