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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 612

  2. anndata anndata Public

    Annotated data.

    Python 607 160

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 228 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 88 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 226 37

Repositories

Showing 10 of 54 repositories
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 4 MPL-2.0 0 9 2 Updated Mar 11, 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 11, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,342 BSD-3-Clause 381 33 (1 issue needs help) 7 Updated Mar 11, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 71 11 16 4 Updated Mar 11, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 45 BSD-3-Clause 19 5 1 Updated Mar 11, 2025
  • squidpy_notebooks Public

    Tutorials for Squidpy

    scverse/squidpy_notebooks’s past year of commit activity
    Jupyter Notebook 30 MIT 19 6 4 Updated Mar 10, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 471 BSD-3-Clause 89 81 (1 issue needs help) 7 Updated Mar 10, 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 46 6 8 Updated Mar 10, 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 176 MIT 25 15 2 Updated Mar 10, 2025
  • prelude-runner Public

    Jupyter notebook runner that executes preludes before each cell

    scverse/prelude-runner’s past year of commit activity
    Python 0 Apache-2.0 0 1 0 Updated Mar 10, 2025
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