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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 482 112

  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 396 66

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 400 73

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 327 39

Repositories

Showing 10 of 251 repositories
  • DRVI Public

    Unsupervised Deep Disentangled Representation of Single-Cell Omics

    theislab/DRVI’s past year of commit activity
    Python 57 BSD-3-Clause 5 8 1 Updated Jan 13, 2026
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    theislab/hadge’s past year of commit activity
    Nextflow 24 MIT 7 13 1 Updated Jan 13, 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 12, 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 0 Updated Jan 12, 2026
  • regvelo Public

    inferring regulatory cellular dynamics

    theislab/regvelo’s past year of commit activity
    Python 62 BSD-3-Clause 6 1 0 Updated Jan 12, 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 24 BSD-3-Clause 2 0 2 Updated Jan 12, 2026
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 10 BSD-3-Clause 1 26 3 Updated Jan 12, 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 3 Updated Jan 12, 2026
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 183 BSD-3-Clause 14 30 5 Updated Jan 12, 2026
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 106 17 49 14 Updated Jan 13, 2026
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