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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 1.3k 279

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 512 114

  3. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 409 72

  4. scib scib Public

    Benchmarking analysis of data integration tools

    Python 430 77

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 361 53

  6. moscot moscot Public

    Multi-omic single-cell optimal transport tools

    Python 216 16

Repositories

Showing 10 of 273 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 31 BSD-3-Clause 2 0 2 Updated Sep 14, 2026
  • spatialdata-db Public
    theislab/spatialdata-db's past year of commit activity
    Jupyter Notebook 12 BSD-3-Clause 1 26 3 Updated Sep 14, 2026
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate's past year of commit activity
    Python 35 BSD-3-Clause 9 2 2 Updated Sep 14, 2026
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot's past year of commit activity
    Python 216 BSD-3-Clause 16 32 5 Updated Sep 14, 2026
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri's past year of commit activity
    Python 153 GPL-3.0 19 11 1 Updated Sep 14, 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 12 MIT 1 0 2 Updated Sep 14, 2026
  • interscale Public

    InterScale: multi-scale cellular interaction analysis model for spatial transcriptomics

    theislab/interscale's past year of commit activity
    Python 12 BSD-3-Clause 1 8 2 Updated Sep 14, 2026
  • 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 5 4 1 Updated Sep 14, 2026
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy's past year of commit activity
    Python 361 Apache-2.0 53 17 4 Updated Sep 14, 2026
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow's past year of commit activity
    Python 159 MIT 27 50 18 Updated Sep 14, 2026
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