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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 716

  2. anndata anndata Public

    Annotated data.

    Python 713 182

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 442

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 553 106

  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 73 repositories
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,358 BSD-3-Clause 716 488 (5 issues need help) 77 Updated Feb 27, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 713 BSD-3-Clause 182 183 (4 issues need help) 63 Updated Feb 27, 2026
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 302 MIT 41 13 7 Updated Feb 27, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 154 16 29 6 Updated Feb 27, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 553 BSD-3-Clause 106 66 (1 issue needs help) 21 Updated Feb 26, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,571 BSD-3-Clause 442 14 (1 issue needs help) 10 Updated Feb 26, 2026
  • cellrank Public

    CellRank: dynamics from multi-view single-cell data

    scverse/cellrank’s past year of commit activity
    Python 430 BSD-3-Clause 52 22 5 Updated Feb 26, 2026
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 89 BSD-3-Clause 53 63 12 Updated Feb 26, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler’s past year of commit activity
    Python 257 BSD-3-Clause 35 5 5 Updated Feb 26, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 9 17 1 Updated Feb 26, 2026
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