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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 1.2k 262

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 496 111

  3. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 401 70

  4. scib scib Public

    Benchmarking analysis of data integration tools

    Python 410 75

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 337 44

  6. moscot moscot Public

    Multi-omic single-cell optimal transport tools

    Python 200 17

Repositories

Showing 10 of 256 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 Apr 12, 2026
  • jump-cpg0016-segmentation Public

    Snakemake pipeline used to segment the cpg0016 dataset of the JUMP-Cell Painting Consortium

    theislab/jump-cpg0016-segmentation’s past year of commit activity
    Jupyter Notebook 9 MIT 0 1 1 Updated Apr 11, 2026
  • sctram Public

    Single Cell Trajectory Representation Metrics

    theislab/sctram’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 0 0 0 Updated Apr 10, 2026
  • interscale Public

    InterScale: multi-scale cellular interaction analysis model for spatial transcriptomics

    theislab/interscale’s past year of commit activity
    Python 0 BSD-3-Clause 0 8 1 Updated Apr 10, 2026
  • ehrapy-tutorials Public

    Tutorials for ehrapy

    theislab/ehrapy-tutorials’s past year of commit activity
    Jupyter Notebook 9 Apache-2.0 2 0 0 Updated Apr 10, 2026
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 337 Apache-2.0 44 23 (1 issue needs help) 4 Updated Apr 10, 2026
  • perturbation-metrics Public
    theislab/perturbation-metrics’s past year of commit activity
    Jupyter Notebook 9 BSD-3-Clause 0 0 1 Updated Apr 9, 2026
  • cellink Public

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

    theislab/cellink’s past year of commit activity
    Python 14 Apache-2.0 4 7 5 Updated Apr 8, 2026
  • single-cell-best-practices Public

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

    theislab/single-cell-best-practices’s past year of commit activity
    Jupyter Notebook 1,181 262 74 3 Updated Apr 8, 2026
  • CellFlow2 Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow2’s past year of commit activity
    Python 9 2 0 0 Updated Apr 8, 2026
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