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@scverse

scverse

Foundational tools for omics data in the life sciences
README.md

scverse

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 Public

    Single-cell analysis in Python. Scales to >100M cells.

    Python 2.1k 630

  2. anndata Public

    Annotated data.

    Python 623 164

  3. muon Public

    muon is a multimodal omics Python framework

    Python 235 31

  4. mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 97 19

  5. scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 388

  6. scirpy Public

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

    Python 230 37

Repositories

Showing 10 of 58 repositories
  • spatialdata-plot Public

    Static plotting for spatialdata

    Python 58 BSD-3-Clause 16 84 9 Updated May 13, 2025
  • anndata Public

    Annotated data.

    Python 623 BSD-3-Clause 164 191 (4 issues need help) 53 Updated May 13, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1,372 BSD-3-Clause 388 37 (1 issue needs help) 8 Updated May 13, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    Jupyter Notebook 52 BSD-3-Clause 28 6 5 Updated May 13, 2025
  • anndata-plot Public
    Python 9 MIT 3 1 3 Updated May 13, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    Python 174 MIT 30 31 3 Updated May 13, 2025
  • scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    Python 2,084 BSD-3-Clause 630 497 (6 issues need help) 75 Updated May 13, 2025
  • fast-array-utils Public

    Fast array utilities

    Python 9 MPL-2.0 0 13 2 Updated May 13, 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.

    Python 204 MIT 26 15 3 Updated May 13, 2025
  • spatialdata-notebooks Public
    Jupyter Notebook 53 BSD-3-Clause 20 6 1 Updated May 13, 2025
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