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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 784 221

  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 612 128

  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 357 70

Repositories

Showing 10 of 107 repositories
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 784 BSD-3-Clause 221 192 (4 issues need help) 92 Updated Nov 9, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,212 BSD-2-Clause 99 25 5 Updated Nov 10, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 16 BSD-3-Clause 1 61 7 Updated Nov 10, 2026
  • acumen Public

    A toolkit to test, validate, and improve agentic skills for python packages.

    scverse/acumen's past year of commit activity
    Python 19 MIT 1 1 1 Updated Nov 9, 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 2 Updated Nov 9, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages's past year of commit activity
    Python 42 BSD-3-Clause 100 7 23 Updated Nov 9, 2026
  • scirpy Public

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

    scverse/scirpy's past year of commit activity
    Python 268 BSD-3-Clause 51 36 (2 issues need help) 11 Updated Nov 9, 2026
  • deres Public archive

    Container and visualization for differential expression (and similar) result tables

    scverse/deres's past year of commit activity
    Python 2 BSD-3-Clause 2 6 2 Updated Nov 9, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 408 BSD-3-Clause 108 318 38 Updated Nov 9, 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 0 0 Updated Nov 9, 2026
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