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scverse

Foundational tools for omics data in the life sciences
README.md

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 612

  2. anndata anndata Public

    Annotated data.

    Python 608 160

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 228 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 88 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 382

  6. scirpy scirpy Public

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

    Python 226 37

Repositories

Showing 10 of 54 repositories
  • 202503_hackathon_owkin Public

    Repository to organise the shared hackathon with Owkin in Paris

    scverse/202503_hackathon_owkin’s past year of commit activity
    Jupyter Notebook 0 0 11 0 Updated Mar 12, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 71 11 15 4 Updated Mar 12, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 608 BSD-3-Clause 160 195 (4 issues need help) 55 Updated Mar 12, 2025
  • squidpy_notebooks Public

    Tutorials for Squidpy

    scverse/squidpy_notebooks’s past year of commit activity
    Jupyter Notebook 30 MIT 19 6 4 Updated Mar 12, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 472 BSD-3-Clause 89 81 (1 issue needs help) 6 Updated Mar 12, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,342 BSD-3-Clause 382 33 (1 issue needs help) 8 Updated Mar 12, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 51 BSD-3-Clause 28 8 9 Updated Mar 12, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 263 BSD-3-Clause 54 195 6 Updated Mar 12, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 47 BSD-3-Clause 16 71 7 Updated Mar 11, 2025
  • anndata-tutorials Public

    Use cases for anndata.

    scverse/anndata-tutorials’s past year of commit activity
    Jupyter Notebook 13 13 1 4 Updated Mar 11, 2025
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