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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 777

  2. anndata anndata Public

    Annotated data.

    Python 772 208

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 473

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 598 121

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 394 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 343 66

Repositories

Showing 10 of 97 repositories
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 392 BSD-3-Clause 93 308 19 Updated Sep 16, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 8 BSD-3-Clause 0 17 5 Updated Sep 15, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 598 BSD-3-Clause 121 78 (1 issue needs help) 27 Updated Sep 15, 2026
  • benchmark Public

    Code for running benchmarks

    scverse/benchmark's past year of commit activity
    Rust 4 GPL-3.0 0 7 1 Updated Sep 15, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 6 3 Updated Sep 15, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages's past year of commit activity
    Python 39 BSD-3-Clause 90 6 16 Updated Sep 15, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 394 MIT 52 11 9 Updated Sep 15, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 74 MIT 7 35 54 Updated Sep 15, 2026
  • scvi-tools-site Public

    Website of scVI-Tools: Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools-site's past year of commit activity
    JavaScript 0 2 0 5 Updated Sep 15, 2026
  • stats Public

    scverse statistics

    scverse/stats's past year of commit activity
    TypeScript 4 MIT 0 8 2 Updated Sep 15, 2026
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