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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 610

  2. anndata anndata Public

    Annotated data.

    Python 597 157

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 224 30

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 82 18

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 372

  6. scirpy scirpy Public

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

    Python 223 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 1,323 BSD-3-Clause 372 44 (1 issue needs help) 11 Updated Jan 24, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 68 11 18 4 Updated Jan 24, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 597 BSD-3-Clause 157 197 (4 issues need help) 51 Updated Jan 24, 2025
  • scanpy Public

    Single-cell analysis in Python. Scales to >1M cells.

    scverse/scanpy’s past year of commit activity
    Python 1,980 BSD-3-Clause 610 490 (6 issues need help) 67 Updated Jan 24, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 457 BSD-3-Clause 87 76 (1 issue needs help) 6 Updated Jan 24, 2025
  • scvi-colab Public

    Lightweight helper to install scvi-tools in Google Colab

    scverse/scvi-colab’s past year of commit activity
    Python 0 BSD-3-Clause 1 1 2 Updated Jan 24, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 249 BSD-3-Clause 47 182 6 Updated Jan 22, 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.

    scverse/rapids_singlecell’s past year of commit activity
    Python 168 MIT 23 14 3 Updated Jan 22, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 39 BSD-3-Clause 19 5 0 Updated Jan 21, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 50 BSD-3-Clause 27 8 6 Updated Jan 21, 2025
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