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@scverse

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 >100M cells.

    Python 2k 613

  2. anndata anndata Public

    Annotated data.

    Python 606 160

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 226 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 87 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 381

  6. scirpy scirpy Public

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

    Python 227 37

Repositories

Showing 10 of 52 repositories
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 4 MPL-2.0 0 8 2 Updated Mar 3, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 606 BSD-3-Clause 160 198 (4 issues need help) 54 Updated Mar 3, 2025
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 5 MIT 4 0 1 Updated Mar 3, 2025
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata’s past year of commit activity
    Python 87 BSD-3-Clause 19 16 2 Updated Mar 3, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,339 BSD-3-Clause 381 33 (1 issue needs help) 6 Updated Mar 2, 2025
  • scvi-colab Public

    Lightweight helper to install scvi-tools in Google Colab

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

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 51 BSD-3-Clause 29 8 9 Updated Mar 2, 2025
  • pytometry Public

    Flow & mass cytometry analytics.

    scverse/pytometry’s past year of commit activity
    Python 43 Apache-2.0 9 11 (2 issues need help) 1 Updated Mar 1, 2025
  • ecosystem-packages Public

    Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

    scverse/ecosystem-packages’s past year of commit activity
    Python 20 BSD-3-Clause 45 6 10 Updated Mar 1, 2025
  • muon-tutorials Public

    Tutorials for multimodal omics data analysis

    scverse/muon-tutorials’s past year of commit activity
    Jupyter Notebook 13 BSD-3-Clause 7 6 0 Updated Feb 28, 2025
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