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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 1k 232

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 465 109

  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 382 63

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 378 70

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 307 36

Repositories

Showing 10 of 236 repositories
  • 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 Sep 15, 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 Sep 15, 2025
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 172 BSD-3-Clause 11 31 5 Updated Sep 15, 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 Sep 15, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 85 14 49 14 Updated Sep 15, 2025
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 5 BSD-3-Clause 1 26 3 Updated Sep 15, 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 1 Updated Sep 15, 2025
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 307 Apache-2.0 36 40 4 Updated Sep 15, 2025
  • mapqc Public

    MapQC - a metric for the evaluation of single-cell query-to-reference mappings

    theislab/mapqc’s past year of commit activity
    Python 9 MIT 1 0 1 Updated Sep 15, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 139 GPL-3.0 19 13 1 Updated Sep 15, 2025
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