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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 615

  2. anndata anndata Public

    Annotated data.

    Python 603 159

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 226 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 87 18

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 378

  6. scirpy scirpy Public

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

    Python 226 36

Repositories

Showing 10 of 52 repositories
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 255 BSD-3-Clause 50 190 4 Updated Feb 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 1,334 BSD-3-Clause 378 44 (1 issue needs help) 15 Updated Feb 24, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 41 BSD-3-Clause 19 5 0 Updated Feb 24, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 49 BSD-3-Clause 32 39 9 Updated Feb 24, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 46 BSD-3-Clause 16 71 7 Updated Feb 23, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 603 BSD-3-Clause 159 196 (4 issues need help) 54 Updated Feb 23, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 155 MIT 26 31 3 Updated Feb 23, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,012 BSD-3-Clause 615 497 (6 issues need help) 70 Updated Feb 21, 2025
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 4 MPL-2.0 0 6 3 Updated Feb 21, 2025
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 5 MIT 4 0 1 Updated Feb 21, 2025
View all repositories

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