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 2.4k 720

  2. anndata anndata Public

    Annotated data.

    Python 720 183

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 443

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 555 108

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 354 86

  6. scirpy scirpy Public

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

    Python 246 43

Repositories

Showing 10 of 76 repositories
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,583 BSD-3-Clause 443 14 (1 issue needs help) 12 Updated Mar 17, 2026
  • annbatch Public

    Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

    scverse/annbatch’s past year of commit activity
    Python 26 MIT 3 22 10 Updated Mar 17, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell’s past year of commit activity
    Python 322 MIT 42 15 7 Updated Mar 16, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 163 16 30 6 Updated Mar 16, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 3 9 17 1 Updated Mar 16, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 34 BSD-3-Clause 69 8 9 Updated Mar 17, 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 Mar 16, 2026
  • cookiecutter-scverse-presentation Public

    Introduction to our template

    scverse/cookiecutter-scverse-presentation’s past year of commit activity
    2 0 0 0 Updated Mar 16, 2026
  • anndata-plot Public
    scverse/anndata-plot’s past year of commit activity
    Python 8 MIT 3 1 4 Updated Mar 16, 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 Mar 16, 2026
View all repositories