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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 789

  2. anndata anndata Public

    Annotated data.

    Python 776 216

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 477

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 601 124

  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
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy's past year of commit activity
    Python 347 MIT 67 9 7 Updated Oct 7, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 601 BSD-3-Clause 124 82 (1 issue needs help) 31 Updated Oct 7, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 11 BSD-3-Clause 0 37 1 Updated Oct 7, 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 14 14 Updated Oct 6, 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 71 MIT 6 23 12 Updated Oct 6, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 399 BSD-3-Clause 99 310 29 Updated Oct 6, 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 2 Updated Oct 6, 2026
  • muon Public

    muon is a multimodal omics Python framework

    scverse/muon's past year of commit activity
    Python 279 BSD-3-Clause 37 9 1 Updated Oct 6, 2026
  • stats Public

    scverse statistics

    scverse/stats's past year of commit activity
    TypeScript 4 MIT 0 8 2 Updated Oct 6, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,702 BSD-3-Clause 477 13 (1 issue needs help) 19 Updated Oct 6, 2026
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