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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 784

  2. anndata anndata Public

    Annotated data.

    Python 775 214

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 476

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 599 123

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 398 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 346 67

Repositories

Showing 10 of 97 repositories
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 76 MIT 7 39 64 Updated Sep 29, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 398 MIT 52 14 11 Updated Sep 29, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 11 BSD-3-Clause 0 37 0 Updated Sep 29, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 599 BSD-3-Clause 123 82 (1 issue needs help) 32 Updated Sep 29, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 4 1 Updated Sep 29, 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 8 Updated Sep 29, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 396 BSD-3-Clause 98 310 28 Updated Sep 29, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,202 BSD-2-Clause 97 26 19 Updated Sep 29, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler's past year of commit activity
    Python 296 BSD-3-Clause 38 1 2 Updated Sep 28, 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 70 MIT 6 25 11 Updated Sep 28, 2026
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