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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 730

  2. anndata anndata Public

    Annotated data.

    Python 729 186

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 445

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 560 110

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 360 87

  6. scirpy scirpy Public

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

    Python 247 43

Repositories

Showing 10 of 78 repositories
  • 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 1 Updated Apr 9, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,407 BSD-3-Clause 730 482 (4 issues need help) 83 Updated Apr 9, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell’s past year of commit activity
    Python 353 MIT 44 14 8 Updated Apr 9, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 729 BSD-3-Clause 186 188 (4 issues need help) 70 Updated Apr 9, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,597 BSD-3-Clause 445 14 (1 issue needs help) 10 Updated Apr 9, 2026
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 64 BSD-3-Clause 32 1 4 Updated Apr 9, 2026
  • scvi-colab Public

    Lightweight helper to install scvi-tools in Google Colab

    scverse/scvi-colab’s past year of commit activity
    Python 2 BSD-3-Clause 1 1 0 Updated Apr 9, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 36 BSD-3-Clause 73 7 7 Updated Apr 9, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy’s past year of commit activity
    Python 304 MIT 54 29 4 Updated Apr 8, 2026
  • session-info2 Public
    scverse/session-info2’s past year of commit activity
    Python 7 MPL-2.0 2 1 0 Updated Apr 8, 2026
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