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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 482

  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 410 57

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 355 70

Repositories

Showing 10 of 107 repositories
  • session-info2 Public
    scverse/session-info2's past year of commit activity
    Python 10 MPL-2.0 2 1 0 Updated Nov 2, 2026
  • cookiecutter-scverse-presentation Public

    Introduction to our template

    scverse/cookiecutter-scverse-presentation's past year of commit activity
    2 0 0 0 Updated Nov 2, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 5 2 Updated Nov 2, 2026
  • pandas-uuid Public

    Pandas ExtensionArray / ExtensionDType for UUID

    scverse/pandas-uuid's past year of commit activity
    Python 3 MPL-2.0 0 5 0 Updated Nov 2, 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 Nov 2, 2026
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials's past year of commit activity
    Python 23 BSD-3-Clause 18 12 7 Updated Nov 2, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages's past year of commit activity
    Python 43 BSD-3-Clause 100 7 24 Updated Nov 2, 2026
  • zulip-bots Public

    Repository for zulip bots for scverse.zulipchat.com

    scverse/zulip-bots's past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Nov 2, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 202 24 51 11 Updated Nov 2, 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 6 Updated Nov 2, 2026
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