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@scverse

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 805

  2. anndata anndata Public

    Annotated data.

    Python 782 220

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 483

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 611 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 406 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 353 68

Repositories

Showing 10 of 100 repositories
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 5 1 Updated Oct 25, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 199 24 51 13 Updated Oct 25, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 611 BSD-3-Clause 128 82 (1 issue needs help) 29 Updated Oct 25, 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 5 Updated Oct 25, 2026
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials's past year of commit activity
    Python 23 BSD-3-Clause 18 12 7 Updated Oct 25, 2026
  • scirpy Public

    A scanpy extension to analyse single-cell TCR and BCR data.

    scverse/scirpy's past year of commit activity
    Python 268 BSD-3-Clause 50 36 (2 issues need help) 11 Updated Oct 25, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler's past year of commit activity
    Python 300 BSD-3-Clause 40 1 3 Updated Oct 25, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc's past year of commit activity
    Python 6 BSD-3-Clause 2 6 3 Updated Oct 25, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 5 1 Updated Oct 25, 2026
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse's past year of commit activity
    Python 91 BSD-3-Clause 17 23 3 Updated Oct 25, 2026
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