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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 246

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 481 112

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 411 50

  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 397 73

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 323 38

Repositories

Showing 10 of 249 repositories
  • 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 Dec 21, 2025
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    theislab/hadge’s past year of commit activity
    Nextflow 24 MIT 7 23 1 Updated Dec 21, 2025
  • cellucid Public

    Interactive 3D UMAP viewer that scales to massive datasets.

    theislab/cellucid’s past year of commit activity
    JavaScript 2 0 0 0 Updated Dec 20, 2025
  • huCIRA Public
    theislab/huCIRA’s past year of commit activity
    Python 21 MIT 3 1 0 Updated Dec 20, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 8 Apache-2.0 4 17 1 Updated Dec 19, 2025
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 323 Apache-2.0 38 30 (1 issue needs help) 0 Updated Dec 19, 2025
  • cellink Public

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

    theislab/cellink’s past year of commit activity
    Python 6 Apache-2.0 0 11 2 Updated Dec 19, 2025
  • prophet Public
    theislab/prophet’s past year of commit activity
    Python 38 MIT 3 6 0 Updated Dec 18, 2025
  • single-cell-best-practices Public

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

    theislab/single-cell-best-practices’s past year of commit activity
    Jupyter Notebook 1,088 246 77 2 Updated Dec 17, 2025
  • multimil Public

    Weakly supervised learning uncovers phenotypic signatures in single-cell data

    theislab/multimil’s past year of commit activity
    Python 36 BSD-3-Clause 7 3 1 Updated Dec 17, 2025
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