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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 629

  2. anndata anndata Public

    Annotated data.

    Python 621 164

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 233 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 95 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 388

  6. scirpy scirpy Public

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

    Python 230 37

Repositories

Showing 10 of 57 repositories
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 171 MIT 29 34 4 Updated May 2, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 75 12 16 3 Updated May 2, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,371 BSD-3-Clause 388 40 (1 issue needs help) 10 Updated May 2, 2025
  • ecosystem-packages Public

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

    scverse/ecosystem-packages’s past year of commit activity
    Python 22 BSD-3-Clause 49 7 9 Updated May 1, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 486 BSD-3-Clause 95 83 (1 issue needs help) 11 Updated Apr 30, 2025
  • squidpy_notebooks Public

    Tutorials for Squidpy

    scverse/squidpy_notebooks’s past year of commit activity
    Jupyter Notebook 32 MIT 21 6 7 Updated Apr 30, 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 199 MIT 26 16 3 Updated Apr 30, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 57 BSD-3-Clause 16 76 9 Updated Apr 30, 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 8 12 Updated Apr 29, 2025
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 9 MPL-2.0 0 12 3 Updated Apr 29, 2025
View all repositories

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