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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 691

  2. anndata anndata Public

    Annotated data.

    Python 699 180

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 433

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 546 101

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 338 78

  6. scirpy scirpy Public

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

    Python 243 41

Repositories

Showing 10 of 71 repositories
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 243 BSD-3-Clause 41 39 (3 issues need help) 6 Updated Jan 10, 2026
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 12 MIT 2 0 0 Updated Jan 9, 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 22 MIT 3 20 5 Updated Jan 9, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 699 BSD-3-Clause 180 198 (4 issues need help) 66 Updated Jan 9, 2026
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 86 BSD-3-Clause 52 57 14 Updated Jan 9, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy’s past year of commit activity
    Python 260 MIT 42 30 4 Updated Jan 9, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 546 BSD-3-Clause 101 74 (1 issue needs help) 17 Updated Jan 8, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,530 BSD-3-Clause 432 18 (1 issue needs help) 10 Updated Jan 8, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,317 BSD-3-Clause 691 488 (5 issues need help) 77 Updated Jan 7, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 338 BSD-3-Clause 78 255 7 Updated Jan 7, 2026
View all repositories