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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 >1M cells.

    Python 2k 607

  2. anndata anndata Public

    Annotated data.

    Python 589 157

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 223 30

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 80 17

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 366

  6. scirpy scirpy Public

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

    Python 222 36

Repositories

Showing 10 of 51 repositories
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 38 BSD-3-Clause 14 64 4 Updated Jan 4, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 245 BSD-3-Clause 47 182 13 Updated Jan 4, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 45 BSD-3-Clause 29 46 12 Updated Jan 3, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 39 BSD-3-Clause 19 6 4 Updated Jan 3, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,282 BSD-3-Clause 366 43 (1 issue needs help) 8 Updated Jan 2, 2025
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 1 6 17 2 Updated Jan 1, 2025
  • ecosystem-packages Public

    Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

    scverse/ecosystem-packages’s past year of commit activity
    Python 19 BSD-3-Clause 40 6 6 Updated Jan 1, 2025
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 48 BSD-3-Clause 25 8 6 Updated Dec 31, 2024
  • 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 161 MIT 23 15 3 Updated Dec 30, 2024
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 4 MIT 1 0 0 Updated Dec 30, 2024
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