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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:

Pinned Loading

  1. scanpy scanpy Public

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

    Python 2.4k 717

  2. anndata anndata Public

    Annotated data.

    Python 714 182

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 444

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 553 107

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 352 83

  6. scirpy scirpy Public

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

    Python 246 42

Repositories

Showing 10 of 74 repositories
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 553 BSD-3-Clause 107 64 (1 issue needs help) 24 Updated Mar 3, 2026
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 303 MIT 41 13 7 Updated Mar 3, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,574 BSD-3-Clause 444 14 (1 issue needs help) 9 Updated Mar 3, 2026
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 63 BSD-3-Clause 31 1 4 Updated Mar 3, 2026
  • integration-testing Public

    A repo for integration testing core packages against upstream core packages

    scverse/integration-testing’s past year of commit activity
    0 MIT 0 1 1 Updated Mar 3, 2026
  • stats Public

    Statistics for the scverse.

    scverse/stats’s past year of commit activity
    TypeScript 3 MIT 0 7 0 Updated Mar 3, 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 24 MIT 3 21 10 Updated Mar 3, 2026
  • cookiecutter-scverse-instance Public

    Example repository generated from https://github.com/scverse/cookiecutter-scverse?target=https://github.com. 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 2 Updated Mar 3, 2026
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 89 BSD-3-Clause 17 22 3 Updated Mar 3, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 9 17 1 Updated Mar 3, 2026
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