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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 805

  2. anndata anndata Public

    Annotated data.

    Python 782 220

  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 611 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 406 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 353 68

Repositories

Showing 10 of 100 repositories
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,717 BSD-3-Clause 483 16 (1 issue needs help) 14 Updated Oct 25, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 406 MIT 54 13 15 Updated Oct 25, 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 Oct 25, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 5 2 Updated Oct 25, 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 11 Updated Oct 24, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 199 24 49 12 Updated Oct 24, 2026
  • sp-ops Public

    Prototype schema and APIs for OPS support in SpatialData

    scverse/sp-ops's past year of commit activity
    1 BSD-3-Clause 1 0 10 Updated Oct 24, 2026
  • acumen Public

    A toolkit to test, validate, and improve agentic skills.

    scverse/acumen's past year of commit activity
    Python 18 MIT 1 2 1 Updated Oct 24, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler's past year of commit activity
    Python 300 BSD-3-Clause 40 1 2 Updated Oct 24, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,594 BSD-3-Clause 805 449 (3 issues need help) 113 Updated Oct 23, 2026
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