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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 791

  2. anndata anndata Public

    Annotated data.

    Python 777 219

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 478

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 604 123

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 400 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 347 67

Repositories

Showing 10 of 97 repositories
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,705 BSD-3-Clause 478 13 (1 issue needs help) 15 Updated Oct 11, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 3 2 Updated Oct 11, 2026
  • acumen Public

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

    scverse/acumen's past year of commit activity
    Python 10 MIT 1 2 2 Updated Oct 11, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 400 MIT 52 12 14 Updated Oct 11, 2026
  • rapids-singlecell-tutorials Public
    scverse/rapids-singlecell-tutorials's past year of commit activity
    Jupyter Notebook 12 MIT 4 0 0 Updated Oct 11, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages's past year of commit activity
    Python 39 BSD-3-Clause 92 6 18 Updated Oct 11, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 3 0 Updated Oct 11, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 81 MIT 8 40 67 Updated Oct 10, 2026
  • stats Public

    scverse statistics

    scverse/stats's past year of commit activity
    TypeScript 4 MIT 0 9 3 Updated Oct 10, 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 7 Updated Oct 10, 2026
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