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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 2.3k 687

  2. anndata anndata Public

    Annotated data.

    Python 696 180

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 428

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 544 100

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 334 78

  6. scirpy scirpy Public

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

    Python 242 41

Repositories

Showing 10 of 71 repositories
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 696 BSD-3-Clause 180 211 (4 issues need help) 68 Updated Dec 24, 2025
  • 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 3 Updated Dec 24, 2025
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 87 BSD-3-Clause 15 20 1 Updated Dec 24, 2025
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 31 BSD-3-Clause 64 7 9 Updated Dec 24, 2025
  • SnapATAC2 Public

    Single-cell epigenomics analysis tools

    scverse/SnapATAC2’s past year of commit activity
    Python 301 MIT 37 63 1 Updated Dec 24, 2025
  • pandas-uuid Public

    Pandas ExtensionArray / ExtensionDType for UUID

    scverse/pandas-uuid’s past year of commit activity
    Python 1 MPL-2.0 0 7 1 Updated Dec 23, 2025
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler’s past year of commit activity
    Python 245 BSD-3-Clause 34 4 4 Updated Dec 23, 2025
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 284 MIT 39 18 8 Updated Dec 23, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 62 BSD-3-Clause 25 9 1 Updated Dec 23, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 334 BSD-3-Clause 78 255 21 Updated Dec 23, 2025
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