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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 237

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 469 110

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 400 50

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 384 64

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 388 71

  6. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 308 36

Repositories

Showing 10 of 240 repositories
  • 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 21, 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 21, 2025
  • diffxpy Public archive

    Differential expression analysis for single-cell RNA-seq data.

    theislab/diffxpy’s past year of commit activity
    Python 204 BSD-3-Clause 23 102 6 Updated Oct 21, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 89 16 49 16 Updated Oct 20, 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 8 BSD-3-Clause 1 0 2 Updated Oct 20, 2025
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate’s past year of commit activity
    Python 27 BSD-3-Clause 8 4 3 Updated Oct 20, 2025
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot’s past year of commit activity
    Python 175 BSD-3-Clause 12 30 5 Updated Oct 20, 2025
  • mapqc Public

    MapQC - a metric for the evaluation of single-cell query-to-reference mappings

    theislab/mapqc’s past year of commit activity
    Python 9 MIT 1 0 2 Updated Oct 20, 2025
  • devVI Public

    Integration of developmental scRNA-seq data

    theislab/devVI’s past year of commit activity
    Python 0 MIT 1 0 2 Updated Oct 20, 2025
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 5 BSD-3-Clause 1 26 3 Updated Oct 20, 2025
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