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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 615

  2. anndata anndata Public

    Annotated data.

    Python 602 159

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 226 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 87 18

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 378

  6. scirpy scirpy Public

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

    Python 226 36

Repositories

Showing 10 of 52 repositories
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 155 MIT 26 32 3 Updated Feb 22, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,012 BSD-3-Clause 615 495 (6 issues need help) 70 Updated Feb 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 1,334 BSD-3-Clause 378 46 (1 issue needs help) 13 Updated Feb 21, 2025
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 3 MPL-2.0 0 6 3 Updated Feb 21, 2025
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 5 MIT 3 0 1 Updated Feb 21, 2025
  • integration-testing Public

    A repo for integration testing core packages against upstream core packages

    scverse/integration-testing’s past year of commit activity
    0 MIT 0 2 0 Updated Feb 21, 2025
  • pertpy-tutorials Public
    scverse/pertpy-tutorials’s past year of commit activity
    Jupyter Notebook 6 Apache-2.0 9 0 0 Updated Feb 21, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 466 BSD-3-Clause 89 80 (1 issue needs help) 5 Updated Feb 20, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 602 BSD-3-Clause 159 197 (4 issues need help) 54 Updated Feb 20, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 46 BSD-3-Clause 16 71 7 Updated Feb 19, 2025
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