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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 2.3k 687

  2. anndata anndata Public

    Annotated data.

    Python 696 179

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.5k 429

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 544 102

  5. spatialdata spatialdata Public

    An open and interoperable data framework for spatial omics data

    Python 336 78

  6. scirpy scirpy Public

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

    Python 242 41

Repositories

Showing 10 of 71 repositories
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 63 BSD-3-Clause 25 9 1 Updated Jan 3, 2026
  • napari-spatialdata Public

    Interactive visualization of spatial omics data

    scverse/napari-spatialdata’s past year of commit activity
    Python 73 BSD-3-Clause 23 68 (3 issues need help) 7 Updated Jan 1, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 336 BSD-3-Clause 78 253 20 Updated Jan 1, 2026
  • ecosystem-packages Public

    Registry for scverse ecosystem packages

    scverse/ecosystem-packages’s past year of commit activity
    Python 32 BSD-3-Clause 65 7 11 Updated Jan 1, 2026
  • SnapATAC2 Public

    Single-cell epigenomics analysis tools

    scverse/SnapATAC2’s past year of commit activity
    Python 301 MIT 37 60 1 Updated Jan 1, 2026
  • spatialdata-integration-testing Public

    Integration testing for the SpatialData framework

    scverse/spatialdata-integration-testing’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Dec 31, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 73 BSD-3-Clause 18 84 11 Updated Dec 31, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,522 BSD-3-Clause 429 18 (1 issue needs help) 10 Updated Dec 31, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,312 BSD-3-Clause 687 486 (5 issues need help) 77 Updated Dec 30, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 696 BSD-3-Clause 179 210 (4 issues need help) 69 Updated Dec 30, 2025
View all repositories