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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 781

  2. anndata anndata Public

    Annotated data.

    Python 774 210

  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 599 122

  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
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 8 BSD-3-Clause 0 45 3 Updated Sep 27, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 3 1 Updated Sep 27, 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 12 10 Updated Sep 27, 2026
  • scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    scverse/scanpy's past year of commit activity
    Python 2,574 BSD-3-Clause 781 442 (3 issues need help) 95 Updated Sep 27, 2026
  • PyDESeq2 Public

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

    scverse/PyDESeq2's past year of commit activity
    Python 763 MIT 89 36 17 Updated Sep 27, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,697 BSD-3-Clause 477 13 (1 issue needs help) 25 Updated Sep 26, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 599 BSD-3-Clause 122 81 (1 issue needs help) 31 Updated Sep 26, 2026
  • rustar-aligner Public

    A rust implementation of STAR

    scverse/rustar-aligner's past year of commit activity
    Rust 76 MIT 7 35 55 Updated Sep 25, 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 25, 2026
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler's past year of commit activity
    Python 295 BSD-3-Clause 38 3 3 Updated Sep 25, 2026
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