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@theislab

Theis Lab

Institute of Computational Biology

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  1. single-cell-best-practices single-cell-best-practices Public

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

    Jupyter Notebook 1k 232

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 467 109

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 397 50

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 383 64

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 384 71

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 307 36

Repositories

Showing 10 of 238 repositories
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 7 Apache-2.0 3 18 1 Updated Sep 30, 2025
  • CellFlow2 Public Forked from theislab/CellFlow

    Modeling complex perturbations with CellFlow

    theislab/CellFlow2’s past year of commit activity
    Python 1 16 0 0 Updated Sep 30, 2025
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 6 0 1 0 Updated Sep 30, 2025
  • multimil Public

    Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases

    theislab/multimil’s past year of commit activity
    Python 34 BSD-3-Clause 6 10 1 Updated Sep 30, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 140 GPL-3.0 19 13 0 Updated Sep 30, 2025
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 307 Apache-2.0 36 33 (1 issue needs help) 3 Updated Sep 30, 2025
  • 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 6 2 0 Updated Sep 30, 2025
  • scproto Public

    Interpretable self-supervised prototype learning for denoising and integrating single-cell transcriptomic data via biologically meaningful metacells.

    theislab/scproto’s past year of commit activity
    Jupyter Notebook 4 1 0 0 Updated Sep 30, 2025
  • troutpy Public

    Package for the analysis of Transcripts outside segmented cells in ST data

    theislab/troutpy’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 1 0 2 Updated Sep 29, 2025
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 174 BSD-3-Clause 11 30 5 Updated Sep 29, 2025
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