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@theislab

Theis Lab

Theis Lab at Institute of Computational Biology, Helmholtz Munich

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

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

    Jupyter Notebook 1.1k 247

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 484 112

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 411 51

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 397 66

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 400 74

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 328 40

Repositories

Showing 10 of 251 repositories
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 8 Apache-2.0 5 12 2 Updated Jan 19, 2026
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 143 GPL-3.0 19 13 0 Updated Jan 19, 2026
  • troutpy Public

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

    theislab/troutpy’s past year of commit activity
    Jupyter Notebook 25 BSD-3-Clause 2 0 2 Updated Jan 19, 2026
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 10 BSD-3-Clause 1 26 3 Updated Jan 19, 2026
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 183 BSD-3-Clause 15 30 5 Updated Jan 19, 2026
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate’s past year of commit activity
    Python 30 BSD-3-Clause 9 5 2 Updated Jan 19, 2026
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 328 Apache-2.0 40 28 (1 issue needs help) 2 Updated Jan 19, 2026
  • 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 5 3 1 Updated Jan 19, 2026
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 109 18 49 15 Updated Jan 20, 2026
  • 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 2 Updated Jan 19, 2026
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