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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:

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  1. scanpy scanpy Public

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

    Python 2.1k 622

  2. anndata anndata Public

    Annotated data.

    Python 616 162

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 231 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 93 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.4k 384

  6. scirpy scirpy Public

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

    Python 230 38

Repositories

Showing 10 of 57 repositories
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 75 12 17 6 Updated Apr 16, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 57 BSD-3-Clause 33 46 14 Updated Apr 15, 2025
  • pertpy Public

    Perturbation Analysis in the scverse ecosystem.

    scverse/pertpy’s past year of commit activity
    Python 169 MIT 29 31 3 Updated Apr 15, 2025
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 616 BSD-3-Clause 162 192 (4 issues need help) 54 Updated Apr 15, 2025
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 2,066 BSD-3-Clause 622 495 (6 issues need help) 74 Updated Apr 15, 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 189 MIT 26 15 3 Updated Apr 15, 2025
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 6 MPL-2.0 0 11 2 Updated Apr 15, 2025
  • ecosystem-packages Public

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

    scverse/ecosystem-packages’s past year of commit activity
    Python 21 BSD-3-Clause 46 7 7 Updated Apr 15, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 52 BSD-3-Clause 16 76 10 Updated Apr 14, 2025
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 53 BSD-3-Clause 20 6 1 Updated Apr 14, 2025
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