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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 2.1k 633

  2. anndata anndata Public

    Annotated data.

    Python 624 164

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 235 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 98 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 388

  6. scirpy scirpy Public

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

    Python 230 37

Repositories

Showing 10 of 58 repositories
  • rapids_singlecell Public

    Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

    scverse/rapids_singlecell’s past year of commit activity
    Python 205 MIT 26 15 3 Updated May 18, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 278 BSD-3-Clause 61 209 18 Updated May 18, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,375 BSD-3-Clause 388 36 (1 issue needs help) 8 Updated May 18, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 487 BSD-3-Clause 96 81 (1 issue needs help) 10 Updated May 17, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,090 BSD-3-Clause 633 494 (6 issues need help) 72 Updated May 17, 2025
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata’s past year of commit activity
    Python 98 BSD-3-Clause 19 13 2 Updated May 17, 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 4 BSD-3-Clause 3 0 1 Updated May 16, 2025
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 77 BSD-3-Clause 11 22 1 Updated May 16, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 624 BSD-3-Clause 164 192 (4 issues need help) 56 Updated May 16, 2025
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials’s past year of commit activity
    Python 16 BSD-3-Clause 13 11 6 Updated May 15, 2025
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