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scverse

Foundational tools for omics data in the life sciences
README.md

scverse

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 2.3k 682

  2. anndata anndata Public

    Annotated data.

    Python 689 179

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 423

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 538 98

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 332 75

  6. scirpy scirpy Public

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

    Python 242 41

Repositories

Showing 10 of 68 repositories
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 62 BSD-3-Clause 26 9 3 Updated Nov 30, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,512 BSD-3-Clause 423 24 (1 issue needs help) 12 Updated Nov 30, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 538 BSD-3-Clause 98 73 (1 issue needs help) 16 Updated Nov 29, 2025
  • rapids_singlecell Public

    rapids_singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids_singlecell’s past year of commit activity
    Python 279 MIT 36 15 9 Updated Nov 28, 2025
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 31 BSD-3-Clause 61 7 15 Updated Nov 28, 2025
  • Muon.jl Public

    Muon for Julia

    scverse/Muon.jl’s past year of commit activity
    Julia 27 BSD-3-Clause 6 1 (1 issue needs help) 0 Updated Nov 28, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 130 14 26 6 Updated Nov 28, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 57 BSD-3-Clause 30 4 5 Updated Nov 26, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 80 BSD-3-Clause 51 61 18 Updated Nov 26, 2025
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 11 MIT 2 0 0 Updated Nov 26, 2025
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