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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 2k 615

  2. anndata anndata Public

    Annotated data.

    Python 612 160

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 230 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 91 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 382

  6. scirpy scirpy Public

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

    Python 227 37

Repositories

Showing 10 of 57 repositories
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 612 BSD-3-Clause 160 192 (4 issues need help) 56 Updated Mar 21, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,045 BSD-3-Clause 615 496 (6 issues need help) 74 Updated Mar 21, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 49 BSD-3-Clause 16 73 6 Updated Mar 21, 2025
  • 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 2 BSD-3-Clause 3 0 1 Updated Mar 21, 2025
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 75 BSD-3-Clause 11 18 1 Updated Mar 21, 2025
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials’s past year of commit activity
    Python 16 BSD-3-Clause 13 11 5 Updated Mar 21, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,351 BSD-3-Clause 382 34 (1 issue needs help) 12 Updated Mar 21, 2025
  • anndata-plot Public
    scverse/anndata-plot’s past year of commit activity
    Python 9 MIT 1 1 3 Updated Mar 19, 2025
  • deres Public

    Container and visualization for differential expression (and similar) result tables

    scverse/deres’s past year of commit activity
    Python 1 BSD-3-Clause 0 6 0 Updated Mar 19, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 165 MIT 27 33 4 Updated Mar 18, 2025
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