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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:

Pinned Loading

  1. scanpy scanpy Public

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

    Python 2.3k 708

  2. anndata anndata Public

    Annotated data.

    Python 707 181

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 436

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 550 104

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 343 80

  6. scirpy scirpy Public

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

    Python 245 42

Repositories

Showing 10 of 71 repositories
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,343 BSD-3-Clause 708 492 (5 issues need help) 79 Updated Feb 5, 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 19 6 Updated Feb 5, 2026
  • pandas-uuid Public

    Pandas ExtensionArray / ExtensionDType for UUID

    scverse/pandas-uuid’s past year of commit activity
    Python 2 MPL-2.0 0 5 2 Updated Feb 5, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 707 BSD-3-Clause 181 199 (4 issues need help) 67 Updated Feb 4, 2026
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 296 MIT 41 14 6 Updated Feb 4, 2026
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 88 BSD-3-Clause 51 62 11 Updated Feb 4, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 343 BSD-3-Clause 80 256 8 Updated Feb 3, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 550 BSD-3-Clause 104 77 (1 issue needs help) 18 Updated Feb 3, 2026
  • Muon.jl Public

    Muon for Julia

    scverse/Muon.jl’s past year of commit activity
    Julia 28 BSD-3-Clause 6 1 (1 issue needs help) 0 Updated Feb 3, 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 3, 2026
View all repositories