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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 800

  2. anndata anndata Public

    Annotated data.

    Python 780 219

  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 610 127

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 404 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 352 68

Repositories

Showing 10 of 97 repositories
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 199 23 44 11 Updated Oct 21, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 404 MIT 54 13 15 Updated Oct 21, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy's past year of commit activity
    Python 352 MIT 68 10 8 Updated Oct 21, 2026
  • pertpy-tutorials Public
    scverse/pertpy-tutorials's past year of commit activity
    Jupyter Notebook 11 Apache-2.0 13 0 2 Updated Oct 21, 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 72 MIT 6 23 12 Updated Oct 21, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,715 BSD-3-Clause 483 13 (1 issue needs help) 13 Updated Oct 21, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 5 1 Updated Oct 21, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 780 BSD-3-Clause 219 186 (4 issues need help) 91 Updated Oct 21, 2026
  • anndata-rs Public
    scverse/anndata-rs's past year of commit activity
    Rust 51 BSD-3-Clause 16 11 3 Updated Oct 21, 2026
  • integration-testing Public

    A repo for integration testing core packages against upstream core packages

    scverse/integration-testing's past year of commit activity
    1 MIT 0 2 1 Updated Oct 21, 2026
View all repositories

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