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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 612

  2. anndata anndata Public

    Annotated data.

    Python 598 157

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 224 30

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 84 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 374

  6. scirpy scirpy Public

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

    Python 224 36

Repositories

Showing 10 of 52 repositories
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 41 BSD-3-Clause 19 5 1 Updated Feb 4, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,325 BSD-3-Clause 374 45 (1 issue needs help) 14 Updated Feb 3, 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 27 8 6 Updated Feb 3, 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 168 MIT 25 15 3 Updated Feb 3, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 43 BSD-3-Clause 15 67 4 Updated Feb 3, 2025
  • simple-scvi Public

    Simple scVI implementation

    scverse/simple-scvi’s past year of commit activity
    Python 10 BSD-3-Clause 4 0 2 Updated Feb 3, 2025
  • pytometry Public

    Flow & mass cytometry analytics.

    scverse/pytometry’s past year of commit activity
    Python 43 Apache-2.0 8 11 (2 issues need help) 1 Updated Feb 3, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy’s past year of commit activity
    Python 459 BSD-3-Clause 88 76 (1 issue needs help) 7 Updated Feb 3, 2025
  • scirpy Public

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

    scverse/scirpy’s past year of commit activity
    Python 224 BSD-3-Clause 36 40 (5 issues need help) 6 Updated Feb 3, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 48 BSD-3-Clause 32 40 11 Updated Feb 3, 2025
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