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scverse

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

scverse

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:

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  1. scanpy scanpy Public

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

    Python 2.4k 736

  2. anndata anndata Public

    Annotated data.

    Python 732 189

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 446

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 562 113

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 362 87

  6. scirpy scirpy Public

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

    Python 247 44

Repositories

Showing 10 of 79 repositories
  • event-template Public template
    scverse/event-template’s past year of commit activity
    SCSS 0 0 0 0 Updated Apr 17, 2026
  • annbatch Public

    Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

    scverse/annbatch’s past year of commit activity
    Python 50 MIT 3 26 8 Updated Apr 17, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,422 BSD-3-Clause 736 479 (4 issues need help) 83 Updated Apr 17, 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 4 Updated Apr 17, 2026
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 90 BSD-3-Clause 17 24 6 Updated Apr 17, 2026
  • 2026_04_hackathon_padua Public

    Repository to organize and share code for the scverse Padua Hackathon, April 2026

    scverse/2026_04_hackathon_padua’s past year of commit activity
    Jupyter Notebook 3 0 37 0 Updated Apr 17, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata’s past year of commit activity
    Python 116 BSD-3-Clause 22 11 3 Updated Apr 17, 2026
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 78 BSD-3-Clause 19 23 4 Updated Apr 16, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 732 BSD-3-Clause 189 189 (4 issues need help) 68 Updated Apr 16, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,601 BSD-3-Clause 446 17 (1 issue needs help) 11 Updated Apr 16, 2026
View all repositories

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