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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 83 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 Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 249 BSD-3-Clause 47 188 7 Updated Jan 31, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 40 BSD-3-Clause 19 5 1 Updated Jan 31, 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) 6 Updated Jan 30, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 148 MIT 25 34 3 Updated Jan 30, 2025
  • muon Public

    muon is a multimodal omics Python framework

    scverse/muon’s past year of commit activity
    Python 224 BSD-3-Clause 30 38 (1 issue needs help) 5 Updated Jan 30, 2025
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,323 BSD-3-Clause 374 45 (1 issue needs help) 13 Updated Jan 30, 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) 5 Updated Jan 30, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 598 BSD-3-Clause 157 197 (4 issues need help) 53 Updated Jan 29, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 47 BSD-3-Clause 32 44 11 Updated Jan 28, 2025
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 1 6 16 2 Updated Jan 28, 2025
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