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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 685

  2. anndata anndata Public

    Annotated data.

    Python 692 181

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 425

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 543 100

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 332 78

  6. scirpy scirpy Public

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

    Python 242 41

Repositories

Showing 10 of 69 repositories
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy’s past year of commit activity
    Python 218 MIT 39 31 4 Updated Dec 13, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,514 BSD-3-Clause 425 16 (1 issue needs help) 9 Updated Dec 13, 2025
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 281 MIT 39 15 9 Updated Dec 12, 2025
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 242 BSD-3-Clause 41 38 (3 issues need help) 4 Updated Dec 12, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 132 14 30 11 Updated Dec 12, 2025
  • pandas-uuid Public

    Pandas ExtensionArray / ExtensionDType for UUID

    scverse/pandas-uuid’s past year of commit activity
    Python 1 MPL-2.0 0 2 1 Updated Dec 12, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 692 BSD-3-Clause 181 209 (4 issues need help) 69 Updated Dec 12, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,286 BSD-3-Clause 685 483 (5 issues need help) 73 Updated Dec 12, 2025
  • 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 18 MIT 2 22 2 Updated Dec 12, 2025
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler’s past year of commit activity
    Python 242 BSD-3-Clause 35 1 1 Updated Dec 12, 2025
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