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scverse

Foundational tools for omics data in the life sciences
README.md

scverse

Welcome to 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 2.4k 738

  2. anndata anndata Public

    Annotated data.

    Python 732 189

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.6k 446

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 563 113

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 362 87

  6. scirpy scirpy Public

    A scanpy extension to analyse single-cell TCR and BCR data.

    Python 247 45

Repositories

Showing 10 of 79 repositories
  • decoupler Public

    Python package to perform enrichment analysis from omics data.

    scverse/decoupler’s past year of commit activity
    Python 266 BSD-3-Clause 35 1 1 Updated Apr 21, 2026
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 732 BSD-3-Clause 189 189 (4 issues need help) 69 Updated Apr 21, 2026
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,426 BSD-3-Clause 738 479 (4 issues need help) 85 Updated Apr 21, 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 53 MIT 3 26 10 Updated Apr 21, 2026
  • PyDESeq2 Public

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

    scverse/PyDESeq2’s past year of commit activity
    Python 747 MIT 83 39 10 Updated Apr 21, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell’s past year of commit activity
    Python 355 MIT 43 14 8 Updated Apr 21, 2026
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 12 MIT 3 0 0 Updated Apr 21, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 563 BSD-3-Clause 113 69 (1 issue needs help) 30 Updated Apr 21, 2026
  • scverse-misc Public

    Miscellaneous utility code used by scverse packages

    scverse/scverse-misc’s past year of commit activity
    Python 4 BSD-3-Clause 0 4 1 Updated Apr 21, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata’s past year of commit activity
    Python 117 BSD-3-Clause 22 10 3 Updated Apr 21, 2026
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