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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 627

  2. anndata Public

    Annotated data.

    Python 619 163

  3. muon Public

    muon is a multimodal omics Python framework

    Python 231 31

  4. mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 93 19

  5. scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 387

  6. scirpy Public

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

    Python 230 38

Repositories

Showing 10 of 57 repositories
  • fast-array-utils Public

    Fast array utilities

    Python 9 MPL-2.0 0 11 3 Updated Apr 25, 2025
  • scanpy Public

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

    Python 2,076 BSD-3-Clause 627 497 (6 issues need help) 75 Updated Apr 25, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    Python 57 BSD-3-Clause 16 77 9 Updated Apr 25, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    Python 485 BSD-3-Clause 95 85 (1 issue needs help) 11 Updated Apr 25, 2025
  • anndata Public

    Annotated data.

    Python 619 BSD-3-Clause 163 191 (4 issues need help) 54 Updated Apr 25, 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 196 MIT 26 15 4 Updated Apr 25, 2025
  • rapids_singlecell-notebooks Public
    Jupyter Notebook 8 MIT 2 0 0 Updated Apr 25, 2025
  • scverse.github.io Public

    scverse.org website

    HTML 3 7 17 0 Updated Apr 25, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1,368 BSD-3-Clause 387 41 (1 issue needs help) 10 Updated Apr 24, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    Jupyter Notebook 52 BSD-3-Clause 28 8 12 Updated Apr 23, 2025
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