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@scverse

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 >1M cells.

    Python 2k 612

  2. anndata anndata Public

    Annotated data.

    Python 600 157

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 225 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 84 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 375

  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-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 41 BSD-3-Clause 19 5 1 Updated Feb 7, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 249 BSD-3-Clause 47 190 6 Updated Feb 6, 2025
  • napari-spatialdata Public

    Interactive visualization of spatial omics data

    scverse/napari-spatialdata’s past year of commit activity
    Python 48 BSD-3-Clause 17 53 (3 issues need help) 2 Updated Feb 6, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 68 11 18 2 Updated Feb 6, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,328 BSD-3-Clause 375 45 (1 issue needs help) 14 Updated Feb 6, 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 169 MIT 25 15 4 Updated Feb 6, 2025
  • squidpy_notebooks Public

    Tutorials for Squidpy

    scverse/squidpy_notebooks’s past year of commit activity
    Jupyter Notebook 30 MIT 18 6 2 Updated Feb 5, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 460 BSD-3-Clause 88 76 (1 issue needs help) 7 Updated Feb 5, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 150 MIT 25 34 3 Updated Feb 5, 2025
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 226 BSD-3-Clause 36 40 (5 issues need help) 5 Updated Feb 5, 2025
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