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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 >1M cells.

    Python 2k 611

  2. anndata anndata Public

    Annotated data.

    Python 592 157

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 224 30

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 82 17

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 371

  6. scirpy scirpy Public

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

    Python 223 36

Repositories

Showing 10 of 51 repositories
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,318 BSD-3-Clause 371 43 (1 issue needs help) 11 Updated Jan 21, 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 168 MIT 23 14 3 Updated Jan 22, 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 47 179 7 Updated Jan 22, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 39 BSD-3-Clause 19 5 0 Updated Jan 21, 2025
  • scanpy Public

    Single-cell analysis in Python. Scales to >1M cells.

    scverse/scanpy’s past year of commit activity
    Python 1,976 BSD-3-Clause 611 505 (6 issues need help) 70 Updated Jan 21, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 456 BSD-3-Clause 86 73 (1 issue needs help) 5 Updated Jan 21, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 50 BSD-3-Clause 27 8 6 Updated Jan 21, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 592 BSD-3-Clause 157 196 (4 issues need help) 52 Updated Jan 21, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 45 BSD-3-Clause 31 42 10 Updated Jan 21, 2025
  • napari-spatialdata Public

    Interactive visualization of spatial omics data

    scverse/napari-spatialdata’s past year of commit activity
    Python 45 BSD-3-Clause 17 52 (3 issues need help) 0 Updated Jan 21, 2025
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