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@scverse

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 779

  2. anndata anndata Public

    Annotated data.

    Python 773 209

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 474

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 598 121

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 394 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 346 67

Repositories

Showing 10 of 97 repositories
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 8 BSD-3-Clause 0 44 2 Updated Sep 20, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 394 MIT 52 11 10 Updated Sep 20, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 3 2 Updated Sep 20, 2026
  • PyDESeq2 Public

    A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

    scverse/PyDESeq2's past year of commit activity
    Python 761 MIT 90 36 14 Updated Sep 20, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 6 3 Updated Sep 19, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 598 BSD-3-Clause 121 79 (1 issue needs help) 27 Updated Sep 18, 2026
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot's past year of commit activity
    Python 86 BSD-3-Clause 21 20 6 Updated Sep 18, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 75 MIT 7 35 55 Updated Sep 18, 2026
  • event-template Public template
    scverse/event-template's past year of commit activity
    SCSS 0 BSD-3-Clause 0 0 0 Updated Sep 18, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc's past year of commit activity
    Python 5 BSD-3-Clause 2 7 3 Updated Sep 18, 2026
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