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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 485 112

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 413 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 402 74

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 329 40

Repositories

Showing 10 of 251 repositories
  • cellink Public

    Scalable framework for integrating single-cell omics with genetic data using AnnData.

    theislab/cellink’s past year of commit activity
    Python 11 Apache-2.0 2 5 3 Updated Jan 27, 2026
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 8 0 1 0 Updated Jan 27, 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 4 0 Updated Jan 27, 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 27, 2026
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    theislab/hadge’s past year of commit activity
    Nextflow 24 MIT 7 16 1 Updated Jan 27, 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 26, 2026
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 10 BSD-3-Clause 1 26 3 Updated Jan 26, 2026
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 185 BSD-3-Clause 16 30 5 Updated Jan 26, 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 26, 2026
  • DRVI Public

    Unsupervised Deep Disentangled Representation of Single-Cell Omics

    theislab/DRVI’s past year of commit activity
    Python 59 BSD-3-Clause 5 8 3 Updated Jan 26, 2026
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