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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 622

  2. anndata anndata Public

    Annotated data.

    Python 614 162

  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 92 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 384

  6. scirpy scirpy Public

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

    Python 230 38

Repositories

Showing 10 of 57 repositories
  • ecosystem-packages Public

    Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

    scverse/ecosystem-packages’s past year of commit activity
    Python 21 BSD-3-Clause 46 7 7 Updated Apr 15, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 169 MIT 29 33 3 Updated Apr 14, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 51 BSD-3-Clause 16 76 10 Updated Apr 14, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 53 BSD-3-Clause 20 6 1 Updated Apr 14, 2025
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 7 17 0 Updated Apr 14, 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 188 MIT 26 15 2 Updated Apr 14, 2025
  • prelude-runner Public

    Jupyter notebook runner that executes preludes before each cell

    scverse/prelude-runner’s past year of commit activity
    Python 1 Apache-2.0 0 1 0 Updated Apr 14, 2025
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials’s past year of commit activity
    Python 16 BSD-3-Clause 13 11 6 Updated Apr 14, 2025
  • scanpy-tutorials Public

    Scanpy Tutorials.

    scverse/scanpy-tutorials’s past year of commit activity
    Jupyter Notebook 209 BSD-3-Clause 117 15 (1 issue needs help) 1 Updated Apr 14, 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 3 Updated Apr 14, 2025
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