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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:

Pinned Loading

  1. scanpy scanpy Public

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

    Python 2.1k 626

  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 386

  6. scirpy scirpy Public

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

    Python 230 38

Repositories

Showing 10 of 57 repositories
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 53 BSD-3-Clause 20 6 0 Updated Apr 21, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 55 BSD-3-Clause 16 78 9 Updated Apr 21, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 617 BSD-3-Clause 163 192 (4 issues need help) 55 Updated Apr 21, 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) 1 Updated Apr 21, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 59 BSD-3-Clause 33 45 14 Updated Apr 21, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 274 BSD-3-Clause 60 206 16 Updated Apr 21, 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 191 MIT 26 15 3 Updated Apr 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 3 BSD-3-Clause 3 0 2 Updated Apr 21, 2025
  • 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 1 Updated Apr 21, 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 Apr 21, 2025
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