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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 796

  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 479

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 608 124

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 402 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 349 68

Repositories

Showing 10 of 97 repositories
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,206 BSD-2-Clause 99 25 3 Updated Oct 15, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,588 BSD-3-Clause 796 447 (3 issues need help) 108 Updated Oct 15, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 86 MIT 9 30 25 Updated Oct 15, 2026
  • benchmark Public

    Code for running benchmarks

    scverse/benchmark's past year of commit activity
    Rust 4 GPL-3.0 0 7 2 Updated Oct 14, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 400 BSD-3-Clause 100 312 26 Updated Oct 14, 2026
  • Muon.jl Public

    Muon for Julia

    scverse/Muon.jl's past year of commit activity
    Julia 30 BSD-3-Clause 6 1 (1 issue needs help) 0 Updated Oct 14, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy's past year of commit activity
    Python 349 MIT 68 11 8 Updated Oct 14, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 780 BSD-3-Clause 219 186 (4 issues need help) 90 Updated Oct 14, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 402 MIT 54 13 14 Updated Oct 14, 2026
  • cellrank Public

    CellRank: dynamics from multi-view single-cell data

    scverse/cellrank's past year of commit activity
    Python 459 BSD-3-Clause 58 2 2 Updated Oct 14, 2026
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