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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 588 156

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 222 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 79 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 35

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 1,277 BSD-3-Clause 366 42 (1 issue needs help) 9 Updated Dec 24, 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 157 MIT 23 15 3 Updated Dec 23, 2024
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 39 BSD-3-Clause 19 6 5 Updated Dec 23, 2024
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 38 BSD-3-Clause 14 65 8 Updated Dec 23, 2024
  • simple-scvi Public

    Simple scVI implementation

    scverse/simple-scvi’s past year of commit activity
    Python 9 BSD-3-Clause 4 0 2 Updated Dec 23, 2024
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 222 BSD-3-Clause 35 39 (5 issues need help) 6 Updated Dec 23, 2024
  • pytometry Public

    Flow & mass cytometry analytics.

    scverse/pytometry’s past year of commit activity
    Python 42 Apache-2.0 9 11 (2 issues need help) 1 Updated Dec 23, 2024
  • cookiecutter-scverse-presentation Public

    Introduction to our template

    scverse/cookiecutter-scverse-presentation’s past year of commit activity
    0 0 0 1 Updated Dec 23, 2024
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 448 BSD-3-Clause 84 70 (1 issue needs help) 5 Updated Dec 23, 2024
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 45 BSD-3-Clause 29 45 13 Updated Dec 23, 2024
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