Skip to content
@scverse

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:

Pinned Loading

  1. scanpy scanpy Public

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

    Python 2.6k 782

  2. anndata anndata Public

    Annotated data.

    Python 775 210

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 477

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 599 122

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 398 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 346 67

Repositories

Showing 10 of 97 repositories
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 199 23 41 12 Updated Sep 28, 2026
  • cookiecutter-scverse-instance Public

    Example repository generated from https://github.com/scverse/cookiecutter-scverse. This repo is updated automatically to match the latest version of the template.

    scverse/cookiecutter-scverse-instance's past year of commit activity
    Python 5 BSD-3-Clause 6 0 5 Updated Sep 28, 2026
  • prelude-runner Public

    Jupyter notebook runner that executes preludes before each cell

    scverse/prelude-runner's past year of commit activity
    Python 1 Apache-2.0 0 1 0 Updated Sep 28, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages's past year of commit activity
    Python 39 BSD-3-Clause 90 6 16 Updated Sep 28, 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 Sep 28, 2026
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials's past year of commit activity
    Python 22 BSD-3-Clause 18 12 7 Updated Sep 28, 2026
  • muon Public

    muon is a multimodal omics Python framework

    scverse/muon's past year of commit activity
    Python 280 BSD-3-Clause 37 9 1 Updated Sep 28, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 8 BSD-3-Clause 0 35 0 Updated Sep 28, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 24 8 0 Updated Sep 28, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc's past year of commit activity
    Python 5 BSD-3-Clause 2 7 3 Updated Sep 28, 2026
View all repositories