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scverse

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

Welcome to scverse®!

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 2.6k 808

  2. anndata anndata Public

    Annotated data.

    Python 786 223

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 483

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 614 129

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 410 55

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 360 71

Repositories

Showing 10 of 108 repositories
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 18 BSD-3-Clause 1 49 8 Updated Nov 13, 2026
  • sp-ops Public

    Prototype schema and APIs for OPS support in SpatialData

    scverse/sp-ops's past year of commit activity
    Python 1 BSD-3-Clause 1 0 9 Updated Nov 13, 2026
  • scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    scverse/scanpy's past year of commit activity
    Python 2,615 BSD-3-Clause 808 427 (3 issues need help) 97 Updated Nov 13, 2026
  • cellrank Public

    CellRank: dynamics from multi-view single-cell data

    scverse/cellrank's past year of commit activity
    Python 460 BSD-3-Clause 58 3 1 Updated Nov 13, 2026
  • spatialdata-spec Public

    Specification for the SpatialData format

    scverse/spatialdata-spec's past year of commit activity
    2 0 2 5 Updated Nov 13, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 410 BSD-3-Clause 108 314 32 Updated Nov 13, 2026
  • infercnvpy Public

    Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

    scverse/infercnvpy's past year of commit activity
    Python 202 BSD-3-Clause 33 16 5 Updated Nov 13, 2026
  • rapids-singlecell-tutorials Public
    scverse/rapids-singlecell-tutorials's past year of commit activity
    Jupyter Notebook 12 MIT 5 0 0 Updated Nov 13, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 4 1 Updated Nov 13, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 135 BSD-3-Clause 28 13 3 Updated Nov 13, 2026
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