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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 >1M cells.

    Python 2k 608

  2. anndata anndata Public

    Annotated data.

    Python 588 157

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 223 30

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 80 17

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 366

  6. scirpy scirpy Public

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

    Python 222 36

Repositories

Showing 10 of 51 repositories
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,281 BSD-3-Clause 366 42 (1 issue needs help) 8 Updated Dec 31, 2024
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 47 BSD-3-Clause 25 8 6 Updated Dec 31, 2024
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 39 BSD-3-Clause 19 6 5 Updated Dec 31, 2024
  • 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 160 MIT 23 15 3 Updated Dec 30, 2024
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 3 MIT 1 0 0 Updated Dec 30, 2024
  • napari-spatialdata Public

    Interactive visualization of spatial omics data

    scverse/napari-spatialdata’s past year of commit activity
    Python 43 BSD-3-Clause 17 52 (3 issues need help) 0 Updated Dec 26, 2024
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 38 BSD-3-Clause 14 64 3 Updated Dec 26, 2024
  • cookiecutter-scverse-instance Public

    Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.

    scverse/cookiecutter-scverse-instance’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 2 Updated Dec 26, 2024
  • cookiecutter-scverse Public

    Cookiecutter template for scverse

    scverse/cookiecutter-scverse’s past year of commit activity
    Python 71 BSD-3-Clause 10 20 1 Updated Dec 26, 2024
  • cookiecutter-scverse-presentation Public

    Introduction to our template

    scverse/cookiecutter-scverse-presentation’s past year of commit activity
    0 0 0 0 Updated Dec 26, 2024
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