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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 >100M cells.

    Python 2k 612

  2. anndata anndata Public

    Annotated data.

    Python 606 160

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 228 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 88 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 381

  6. scirpy scirpy Public

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

    Python 227 37

Repositories

Showing 10 of 54 repositories
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 259 BSD-3-Clause 52 195 5 Updated Mar 10, 2025
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 227 BSD-3-Clause 37 38 (5 issues need help) 4 Updated Mar 9, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,341 BSD-3-Clause 381 33 (1 issue needs help) 5 Updated Mar 9, 2025
  • scvi-colab Public

    Lightweight helper to install scvi-tools in Google Colab

    scverse/scvi-colab’s past year of commit activity
    Python 1 BSD-3-Clause 1 2 0 Updated Mar 9, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 606 BSD-3-Clause 160 196 (4 issues need help) 56 Updated Mar 9, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 47 BSD-3-Clause 16 70 6 Updated Mar 8, 2025
  • 202503_hackathon_owkin Public

    Repository to organise the shared hackathon with Owkin in Paris

    scverse/202503_hackathon_owkin’s past year of commit activity
    0 0 4 0 Updated Mar 8, 2025
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 4 MPL-2.0 0 7 2 Updated Mar 8, 2025
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 72 BSD-3-Clause 11 23 1 Updated Mar 7, 2025
  • anndata-tutorials Public

    Use cases for anndata.

    scverse/anndata-tutorials’s past year of commit activity
    Jupyter Notebook 13 13 1 4 Updated Mar 7, 2025
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