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@theislab

Theis Lab

Institute of Computational Biology

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  1. single-cell-best-practices single-cell-best-practices Public

    https://www.sc-best-practices.org

    Jupyter Notebook 966 224

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 454 110

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 393 50

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 375 62

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 373 69

  6. single-cell-transformer-papers single-cell-transformer-papers Public

    HTML 323 40

Repositories

Showing 10 of 235 repositories
  • regvelo Public

    inferring regulatory cellular dynamics

    theislab/regvelo’s past year of commit activity
    Python 49 BSD-3-Clause 4 1 0 Updated Aug 1, 2025
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 5 0 2 0 Updated Jul 31, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 74 10 46 15 Updated Jul 31, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 137 GPL-3.0 19 14 1 Updated Jul 29, 2025
  • scanpydoc Public

    Collection of Sphinx extensions similar to (but more flexible than) numpydoc

    theislab/scanpydoc’s past year of commit activity
    Python 12 GPL-3.0 6 2 0 Updated Jul 29, 2025
  • cellrank_protocol Public

    Repository accompanying CellRank's Nature Protocols article.

    theislab/cellrank_protocol’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Jul 28, 2025
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate’s past year of commit activity
    Python 27 BSD-3-Clause 8 4 3 Updated Jul 28, 2025
  • troutpy Public

    Package for the analysis of Transcripts outside segmented cells in ST data

    theislab/troutpy’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 1 Updated Jul 28, 2025
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 167 BSD-3-Clause 10 29 5 Updated Jul 29, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 7 Apache-2.0 3 16 1 Updated Jul 29, 2025
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