Skip to content
@scverse

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 2.4k 725

  2. anndata anndata Public

    Annotated data.

    Python 728 184

  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 559 110

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 358 87

  6. scirpy scirpy Public

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

    Python 246 43

Repositories

Showing 10 of 77 repositories
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 728 BSD-3-Clause 184 186 (4 issues need help) 70 Updated Apr 1, 2026
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 76 BSD-3-Clause 18 29 2 Updated Apr 1, 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 28 MIT 3 22 8 Updated Apr 1, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 35 BSD-3-Clause 72 8 6 Updated Apr 1, 2026
  • cellrank Public

    CellRank: dynamics from multi-view single-cell data

    scverse/cellrank’s past year of commit activity
    Python 437 BSD-3-Clause 55 20 2 Updated Apr 1, 2026
  • 202603_hackathon_proteomics Public
    scverse/202603_hackathon_proteomics’s past year of commit activity
    Jupyter Notebook 7 5 3 2 Updated Mar 31, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell’s past year of commit activity
    Python 344 MIT 44 14 9 Updated Mar 31, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 167 16 30 5 Updated Mar 31, 2026
  • cookiecutter-scverse-instance Public

    Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.

    scverse/cookiecutter-scverse-instance’s past year of commit activity
    Python 5 BSD-3-Clause 6 0 6 Updated Mar 31, 2026
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 89 BSD-3-Clause 17 25 8 Updated Mar 31, 2026
View all repositories

Top languages

Loading…

Most used topics

Loading…