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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 805

  2. anndata anndata Public

    Annotated data.

    Python 783 220

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 483

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 611 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 407 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 353 68

Repositories

Showing 10 of 100 repositories
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 13 BSD-3-Clause 0 30 2 Updated Oct 27, 2026
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 783 BSD-3-Clause 220 190 (4 issues need help) 90 Updated Oct 27, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 407 MIT 54 16 17 Updated Oct 27, 2026
  • muon Public

    muon is a multimodal omics Python framework

    scverse/muon's past year of commit activity
    Python 279 BSD-3-Clause 36 9 1 Updated Oct 27, 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) 5 Updated Oct 27, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 200 24 51 12 Updated Oct 27, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 403 BSD-3-Clause 106 314 37 Updated Oct 27, 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 6 3 Updated Oct 27, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 5 2 Updated Oct 27, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages's past year of commit activity
    Python 42 BSD-3-Clause 98 6 22 Updated Oct 27, 2026
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