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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 2.2k 659

  2. anndata anndata Public

    Annotated data.

    Python 651 171

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 402

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 506 97

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 302 70

  6. scirpy scirpy Public

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

    Python 237 39

Repositories

Showing 10 of 63 repositories
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 103 13 15 5 Updated Aug 30, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 302 BSD-3-Clause 70 225 18 Updated Aug 29, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 506 BSD-3-Clause 97 77 (1 issue needs help) 15 Updated Aug 29, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 651 BSD-3-Clause 171 202 (4 issues need help) 63 Updated Aug 29, 2025
  • SnapATAC2 Public

    Single-cell epigenomics analysis tools

    scverse/SnapATAC2’s past year of commit activity
    Python 283 35 57 1 Updated Aug 28, 2025
  • integration-testing Public

    A repo for integration testing core packages against upstream core packages

    scverse/integration-testing’s past year of commit activity
    1 MIT 0 3 2 Updated Aug 28, 2025
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 234 MIT 30 16 5 Updated Aug 27, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 57 BSD-3-Clause 23 8 3 Updated Aug 27, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,429 BSD-3-Clause 402 26 (1 issue needs help) 9 Updated Aug 27, 2025
  • Muon.jl Public

    Muon for Julia

    scverse/Muon.jl’s past year of commit activity
    Julia 27 BSD-3-Clause 6 1 (1 issue needs help) 0 Updated Aug 27, 2025
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