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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 2.1k 627

  2. anndata anndata Public

    Annotated data.

    Python 618 163

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 231 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 93 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 387

  6. scirpy scirpy Public

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

    Python 230 38

Repositories

Showing 10 of 57 repositories
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 9 MPL-2.0 0 11 3 Updated Apr 24, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 618 BSD-3-Clause 163 192 (4 issues need help) 55 Updated Apr 24, 2025
  • rapids_singlecell Public

    Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

    scverse/rapids_singlecell’s past year of commit activity
    Python 195 MIT 26 15 3 Updated Apr 24, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,365 BSD-3-Clause 387 41 (1 issue needs help) 10 Updated Apr 24, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,075 BSD-3-Clause 627 499 (6 issues need help) 77 Updated Apr 24, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 56 BSD-3-Clause 16 77 9 Updated Apr 23, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 52 BSD-3-Clause 28 8 12 Updated Apr 23, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 60 BSD-3-Clause 33 45 14 Updated Apr 23, 2025
  • napari-spatialdata Public

    Interactive visualization of spatial omics data

    scverse/napari-spatialdata’s past year of commit activity
    Python 53 BSD-3-Clause 18 57 (3 issues need help) 1 Updated Apr 23, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 276 BSD-3-Clause 61 206 16 Updated Apr 23, 2025
View all repositories