Skip to content
@scverse

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:

Pinned Loading

  1. scanpy scanpy Public

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

    Python 2.3k 705

  2. anndata anndata Public

    Annotated data.

    Python 707 181

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 435

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 550 104

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 342 80

  6. scirpy scirpy Public

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

    Python 245 42

Repositories

Showing 10 of 71 repositories
  • session-info2 Public
    scverse/session-info2’s past year of commit activity
    Python 7 MPL-2.0 1 1 1 Updated Feb 2, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 550 BSD-3-Clause 104 79 (1 issue needs help) 20 Updated Feb 2, 2026
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials’s past year of commit activity
    Python 19 BSD-3-Clause 15 12 6 Updated Feb 2, 2026
  • scanpy-tutorials Public

    Scanpy Tutorials.

    scverse/scanpy-tutorials’s past year of commit activity
    Jupyter Notebook 234 BSD-3-Clause 120 15 (1 issue needs help) 2 Updated Feb 2, 2026
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 13 MPL-2.0 1 15 (1 issue needs help) 4 Updated Feb 2, 2026
  • anndata-plot Public
    scverse/anndata-plot’s past year of commit activity
    Python 8 MIT 3 1 5 Updated Feb 2, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler’s past year of commit activity
    Python 252 BSD-3-Clause 35 6 4 Updated Feb 2, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata’s past year of commit activity
    Python 106 BSD-3-Clause 21 9 2 Updated Feb 2, 2026
  • formulaic-contrasts Public

    Build contrasts for models defined with formulaic

    scverse/formulaic-contrasts’s past year of commit activity
    Python 12 BSD-3-Clause 2 2 2 Updated Feb 2, 2026
  • Muon.jl Public

    Muon for Julia

    scverse/Muon.jl’s past year of commit activity
    Julia 28 BSD-3-Clause 6 1 (1 issue needs help) 1 Updated Feb 2, 2026
View all repositories