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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 1.1k 243

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 475 112

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 409 51

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 393 65

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 395 73

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 317 38

Repositories

Showing 10 of 244 repositories
  • troutpy Public

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

    theislab/troutpy’s past year of commit activity
    Jupyter Notebook 11 BSD-3-Clause 2 0 2 Updated Dec 1, 2025
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 9 BSD-3-Clause 1 26 3 Updated Dec 1, 2025
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate’s past year of commit activity
    Python 30 BSD-3-Clause 9 4 4 Updated Dec 1, 2025
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 180 BSD-3-Clause 12 32 5 Updated Dec 1, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 8 Apache-2.0 4 16 2 Updated Dec 1, 2025
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 317 Apache-2.0 38 34 (1 issue needs help) 4 Updated Dec 1, 2025
  • scanpydoc Public

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

    theislab/scanpydoc’s past year of commit activity
    Python 11 GPL-3.0 6 3 1 Updated Dec 1, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 99 16 49 13 Updated Dec 1, 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 11 MIT 1 0 1 Updated Dec 1, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 142 GPL-3.0 19 13 1 Updated Dec 1, 2025
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