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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 720

  2. anndata anndata Public

    Annotated data.

    Python 720 183

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 443

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 555 108

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 354 86

  6. scirpy scirpy Public

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

    Python 246 43

Repositories

Showing 10 of 76 repositories
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 9 17 1 Updated Mar 16, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 34 BSD-3-Clause 69 8 10 Updated Mar 16, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,369 BSD-3-Clause 720 484 (4 issues need help) 77 Updated Mar 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 1,582 BSD-3-Clause 443 14 (1 issue needs help) 12 Updated Mar 16, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell’s past year of commit activity
    Python 316 MIT 42 15 7 Updated Mar 15, 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 15, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 163 16 30 6 Updated Mar 14, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Mar 13, 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 26 MIT 3 22 9 Updated Mar 13, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 720 BSD-3-Clause 183 184 (4 issues need help) 66 Updated Mar 13, 2026
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