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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 795

  2. anndata anndata Public

    Annotated data.

    Python 778 220

  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 604 124

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 400 53

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 347 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 12, 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 12, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 83 MIT 8 40 59 Updated Oct 12, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc's past year of commit activity
    Python 6 BSD-3-Clause 2 7 3 Updated Oct 12, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 27 11 3 Updated Oct 12, 2026
  • simple-scvi Public

    Simple scVI implementation

    scverse/simple-scvi's past year of commit activity
    Python 13 BSD-3-Clause 4 0 3 Updated Oct 12, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 604 BSD-3-Clause 123 78 (1 issue needs help) 22 Updated Oct 12, 2026
  • acumen Public

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

    scverse/acumen's past year of commit activity
    Python 16 MIT 1 2 1 Updated Oct 12, 2026
  • genomic-features Public

    Genomic Features in Python from BioConductor's AnnotationHub

    scverse/genomic-features's past year of commit activity
    Python 22 BSD-3-Clause 5 19 8 Updated Oct 12, 2026
  • pytometry Public

    Flow & mass cytometry analytics.

    scverse/pytometry's past year of commit activity
    Python 61 Apache-2.0 15 13 (2 issues need help) 3 Updated Oct 12, 2026
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