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@scverse

scverse

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

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 2k 615

  2. anndata anndata Public

    Annotated data.

    Python 604 159

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 226 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 87 18

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 379

  6. scirpy scirpy Public

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

    Python 227 36

Repositories

Showing 10 of 52 repositories
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 1 6 16 2 Updated Feb 26, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,336 BSD-3-Clause 379 45 (1 issue needs help) 11 Updated Feb 26, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 604 BSD-3-Clause 159 199 (4 issues need help) 55 Updated Feb 26, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 69 11 18 7 Updated Feb 26, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,016 BSD-3-Clause 615 499 (6 issues need help) 72 Updated Feb 26, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 51 BSD-3-Clause 28 8 11 Updated Feb 26, 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 173 MIT 25 15 5 Updated Feb 26, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 156 MIT 26 30 3 Updated Feb 26, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 41 BSD-3-Clause 19 5 1 Updated Feb 25, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 46 BSD-3-Clause 16 71 7 Updated Feb 25, 2025
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