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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 2.3k 683

  2. anndata anndata Public

    Annotated data.

    Python 691 180

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 424

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 541 99

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 332 77

  6. scirpy scirpy Public

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

    Python 242 41

Repositories

Showing 10 of 68 repositories
  • scvi-colab Public

    Lightweight helper to install scvi-tools in Google Colab

    scverse/scvi-colab’s past year of commit activity
    Python 2 BSD-3-Clause 1 1 0 Updated Dec 8, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,514 BSD-3-Clause 424 17 (1 issue needs help) 9 Updated Dec 8, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 57 BSD-3-Clause 30 3 3 Updated Dec 8, 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 5 BSD-3-Clause 5 0 4 Updated Dec 8, 2025
  • simple-scvi Public

    Simple scVI implementation

    scverse/simple-scvi’s past year of commit activity
    Python 12 BSD-3-Clause 4 0 3 Updated Dec 8, 2025
  • plotting_api Public

    Experimenting with a simplified plotting API for scanpy/scirpy

    scverse/plotting_api’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 0 3 2 Updated Dec 8, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 71 BSD-3-Clause 18 85 9 Updated Dec 8, 2025
  • genomic-features Public

    Genomic Features in Python from BioConductor's AnnotationHub

    scverse/genomic-features’s past year of commit activity
    Python 22 BSD-3-Clause 5 19 8 Updated Dec 8, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 541 BSD-3-Clause 99 74 (1 issue needs help) 17 Updated Dec 8, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 62 BSD-3-Clause 26 9 4 Updated Dec 8, 2025
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