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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 719

  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 554 108

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 353 85

  6. scirpy scirpy Public

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

    Python 246 43

Repositories

Showing 10 of 76 repositories
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,368 BSD-3-Clause 719 484 (5 issues need help) 78 Updated Mar 13, 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 21 9 Updated Mar 13, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell’s past year of commit activity
    Python 315 MIT 42 16 7 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
  • SnapATAC2 Public

    Single-cell epigenomics analysis tools

    scverse/SnapATAC2’s past year of commit activity
    Python 311 MIT 39 61 1 Updated Mar 13, 2026
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 74 BSD-3-Clause 18 76 4 Updated Mar 13, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 160 16 30 6 Updated Mar 12, 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 444 14 (1 issue needs help) 11 Updated Mar 12, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 554 BSD-3-Clause 108 64 (1 issue needs help) 23 Updated Mar 12, 2026
View all repositories