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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 611

  2. anndata anndata Public

    Annotated data.

    Python 598 157

  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 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 373

  6. scirpy scirpy Public

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

    Python 224 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 249 BSD-3-Clause 47 185 8 Updated Jan 29, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,323 BSD-3-Clause 373 46 (1 issue needs help) 13 Updated Jan 29, 2025
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 224 BSD-3-Clause 36 40 (5 issues need help) 5 Updated Jan 29, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 457 BSD-3-Clause 88 76 (1 issue needs help) 5 Updated Jan 29, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 598 BSD-3-Clause 157 198 (4 issues need help) 53 Updated Jan 29, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 39 BSD-3-Clause 19 5 0 Updated Jan 29, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 47 BSD-3-Clause 31 43 11 Updated Jan 28, 2025
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 1 6 16 2 Updated Jan 28, 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 24 15 3 Updated Jan 28, 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 28, 2025
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