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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 514 118

  3. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 414 74

  4. scib scib Public

    Benchmarking analysis of data integration tools

    Python 435 79

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 369 54

  6. moscot moscot Public

    Multi-omic single-cell optimal transport tools

    Python 220 16

Repositories

Showing 10 of 278 repositories
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri's past year of commit activity
    Python 154 GPL-3.0 19 11 0 Updated Nov 2, 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 0 0 Updated Nov 2, 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 Nov 2, 2026
  • DRVI Public

    Unsupervised Deep Disentangled Representation of Single-Cell Omics

    theislab/DRVI's past year of commit activity
    Python 83 BSD-3-Clause 6 5 3 Updated Nov 2, 2026
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot's past year of commit activity
    Python 220 BSD-3-Clause 16 32 5 Updated Nov 2, 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 Nov 2, 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 32 BSD-3-Clause 2 0 2 Updated Nov 2, 2026
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow's past year of commit activity
    Python 165 MIT 31 50 18 Updated Nov 2, 2026
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy's past year of commit activity
    Python 369 Apache-2.0 54 4 2 Updated Nov 2, 2026
  • interscale Public

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

    theislab/interscale's past year of commit activity
    Python 14 BSD-3-Clause 2 7 4 Updated Nov 2, 2026
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