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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 635

  2. anndata anndata Public

    Annotated data.

    Python 624 164

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 235 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 98 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 389

  6. scirpy scirpy Public

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

    Python 230 37

Repositories

Showing 10 of 58 repositories
  • 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 205 MIT 26 16 4 Updated May 22, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 52 BSD-3-Clause 28 10 6 Updated May 22, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 175 MIT 30 33 4 Updated May 21, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,092 BSD-3-Clause 635 493 (6 issues need help) 71 Updated May 21, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 58 BSD-3-Clause 17 85 11 Updated May 21, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,377 BSD-3-Clause 389 37 (1 issue needs help) 10 Updated May 21, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 624 BSD-3-Clause 164 192 (4 issues need help) 56 Updated May 20, 2025
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    HTML 3 7 17 0 Updated May 20, 2025
  • ecosystem-packages Public

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

    scverse/ecosystem-packages’s past year of commit activity
    Python 23 BSD-3-Clause 50 7 10 Updated May 20, 2025
  • anndata-tutorials Public

    Use cases for anndata.

    scverse/anndata-tutorials’s past year of commit activity
    Jupyter Notebook 15 13 1 4 Updated May 20, 2025
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