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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 784 220

  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 613 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 408 55

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 357 70

Repositories

Showing 10 of 107 repositories
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 15 BSD-3-Clause 0 42 4 Updated Nov 4, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 406 BSD-3-Clause 108 315 39 Updated Nov 4, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy's past year of commit activity
    Python 357 MIT 70 10 8 Updated Nov 4, 2026
  • repo-health Public

    Automated checks for security and consistency on scverse.org github repositories

    scverse/repo-health's past year of commit activity
    Python 1 MPL-2.0 0 3 5 Updated Nov 4, 2026
  • anndata-rs Public
    scverse/anndata-rs's past year of commit activity
    Rust 51 BSD-3-Clause 15 13 3 Updated Nov 4, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 408 MIT 55 14 11 Updated Nov 4, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,608 BSD-3-Clause 809 441 (3 issues need help) 96 Updated Nov 3, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 202 24 48 11 Updated Nov 3, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 135 BSD-3-Clause 28 10 2 Updated Nov 3, 2026
  • spatialdata-spec Public

    Specification for the SpatialData format

    scverse/spatialdata-spec's past year of commit activity
    0 0 2 3 Updated Nov 3, 2026
View all repositories

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