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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
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 50 BSD-3-Clause 20 6 1 Updated Mar 24, 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 37 (1 issue needs help) 9 Updated Mar 24, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 612 BSD-3-Clause 160 192 (4 issues need help) 57 Updated Mar 24, 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 11 Updated Mar 24, 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 23, 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 23, 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 23, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 55 BSD-3-Clause 33 43 12 Updated Mar 22, 2025
  • anndata-plot Public
    scverse/anndata-plot’s past year of commit activity
    Python 9 MIT 1 1 3 Updated Mar 22, 2025
  • rapids_singlecell Public

    Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

    scverse/rapids_singlecell’s past year of commit activity
    Python 182 MIT 25 15 3 Updated Mar 21, 2025
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