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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 2.1k 625

  2. anndata anndata Public

    Annotated data.

    Python 617 163

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 231 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 93 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 385

  6. scirpy scirpy Public

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

    Python 230 38

Repositories

Showing 10 of 57 repositories
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,362 BSD-3-Clause 385 39 (1 issue needs help) 9 Updated Apr 21, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 52 BSD-3-Clause 28 8 12 Updated Apr 20, 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 3 BSD-3-Clause 3 0 1 Updated Apr 18, 2025
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 76 BSD-3-Clause 11 20 1 Updated Apr 18, 2025
  • 202504_workshop_GSCN Public
    scverse/202504_workshop_GSCN’s past year of commit activity
    Jupyter Notebook 3 0 11 0 Updated Apr 18, 2025
  • napari-spatialdata Public

    Interactive visualization of spatial omics data

    scverse/napari-spatialdata’s past year of commit activity
    Python 52 BSD-3-Clause 17 56 (3 issues need help) 0 Updated Apr 18, 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 1 6 0 Updated Apr 18, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,069 BSD-3-Clause 625 500 (6 issues need help) 75 Updated Apr 17, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 53 BSD-3-Clause 20 6 0 Updated Apr 17, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 55 BSD-3-Clause 16 77 10 Updated Apr 16, 2025
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