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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 709

  2. anndata anndata Public

    Annotated data.

    Python 711 181

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 438

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 551 104

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 351 81

  6. scirpy scirpy Public

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

    Python 245 42

Repositories

Showing 10 of 71 repositories
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 299 MIT 41 13 7 Updated Feb 16, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,345 BSD-3-Clause 709 490 (5 issues need help) 76 Updated Feb 16, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,566 BSD-3-Clause 438 17 (1 issue needs help) 12 Updated Feb 16, 2026
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 88 BSD-3-Clause 52 62 12 Updated Feb 16, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 351 BSD-3-Clause 81 258 10 Updated Feb 16, 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 22 11 Updated Feb 13, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 711 BSD-3-Clause 181 197 (4 issues need help) 63 Updated Feb 13, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata’s past year of commit activity
    Python 108 BSD-3-Clause 21 9 2 Updated Feb 13, 2026
  • scvi-tools-site Public
    scverse/scvi-tools-site’s past year of commit activity
    JavaScript 0 2 0 0 Updated Feb 13, 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 12, 2026
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