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@scverse

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:

Pinned Loading

  1. scanpy Public

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

    Python 2.1k 629

  2. anndata Public

    Annotated data.

    Python 621 164

  3. muon Public

    muon is a multimodal omics Python framework

    Python 234 31

  4. mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 95 19

  5. scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 388

  6. scirpy Public

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

    Python 230 37

Repositories

Showing 10 of 58 repositories
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1,371 BSD-3-Clause 388 40 (1 issue needs help) 11 Updated May 7, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    Python 173 MIT 29 30 3 Updated May 7, 2025
  • anndata Public

    Annotated data.

    Python 621 BSD-3-Clause 164 190 (4 issues need help) 53 Updated May 7, 2025
  • scanpy-tutorials Public

    Scanpy Tutorials.

    Jupyter Notebook 212 BSD-3-Clause 117 15 (1 issue needs help) 2 Updated May 7, 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.

    Python 203 MIT 26 16 3 Updated May 7, 2025
  • rapids_singlecell-notebooks Public
    Jupyter Notebook 8 MIT 2 0 0 Updated May 7, 2025
  • pertpy-tutorials Public
    Jupyter Notebook 9 Apache-2.0 9 0 0 Updated May 6, 2025
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 95 BSD-3-Clause 19 16 3 Updated May 6, 2025
  • squidpy Public

    Spatial Single Cell Analysis in Python

    Python 487 BSD-3-Clause 95 84 (1 issue needs help) 11 Updated May 6, 2025
  • fast-array-utils Public

    Fast array utilities

    Python 9 MPL-2.0 0 12 2 Updated May 6, 2025
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