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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 238

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 470 111

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 403 51

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 387 64

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 389 73

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 310 36

Repositories

Showing 10 of 240 repositories
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 310 Apache-2.0 36 33 (1 issue needs help) 2 Updated Oct 28, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 8 Apache-2.0 4 20 2 Updated Oct 28, 2025
  • rapids_singlecell-reproducibility Public
    theislab/rapids_singlecell-reproducibility’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 1 Updated Oct 28, 2025
  • pertpy-reproducibility Public
    theislab/pertpy-reproducibility’s past year of commit activity
    Jupyter Notebook 3 Apache-2.0 2 0 0 Updated Oct 28, 2025
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 7 0 1 0 Updated Oct 28, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 142 GPL-3.0 19 13 0 Updated Oct 28, 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 Oct 28, 2025
  • scConcept Public

    Contrastive pre-training for technology-agnostic single-cell representations beyond reconstruction

    theislab/scConcept’s past year of commit activity
    Python 6 0 0 0 Updated Oct 27, 2025
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 176 BSD-3-Clause 12 30 5 Updated Oct 27, 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 10 BSD-3-Clause 2 0 2 Updated Oct 27, 2025
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