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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 248

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 484 112

  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 397 66

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 400 74

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 328 40

Repositories

Showing 10 of 252 repositories
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 8 Apache-2.0 5 11 1 Updated Jan 21, 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 21, 2026
  • IVGLMMS Public

    Instrumental variable modeling for LC-MS clinical proteomics

    theislab/IVGLMMS’s past year of commit activity
    0 MIT 0 0 0 Updated Jan 21, 2026
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    theislab/hadge’s past year of commit activity
    Nextflow 24 MIT 7 15 1 Updated Jan 21, 2026
  • idtrack Public

    Time- and Namespace-Aware Identifier Harmonization for Reproducible Workflows

    theislab/idtrack’s past year of commit activity
    Jupyter Notebook 3 BSD-3-Clause 1 1 0 Updated Jan 20, 2026
  • CellFlow2 Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow2’s past year of commit activity
    Python 7 2 0 0 Updated Jan 20, 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 20, 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 19, 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 19, 2026
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 10 BSD-3-Clause 1 26 3 Updated Jan 19, 2026
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