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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 259

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 490 111

  3. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 400 70

  4. scib scib Public

    Benchmarking analysis of data integration tools

    Python 408 75

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 333 41

Repositories

Showing 10 of 253 repositories
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 333 Apache-2.0 41 27 (1 issue needs help) 5 Updated Mar 11, 2026
  • scConcept Public

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

    theislab/scConcept’s past year of commit activity
    Python 23 MIT 4 0 0 Updated Mar 10, 2026
  • huCIRA Public
    theislab/huCIRA’s past year of commit activity
    Python 32 MIT 3 3 2 Updated Mar 10, 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 Mar 10, 2026
  • cellink Public

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

    theislab/cellink’s past year of commit activity
    Python 13 Apache-2.0 2 5 4 Updated Mar 10, 2026
  • cellflow_reproducibility Public

    Reproducibility repository for CellFlow

    theislab/cellflow_reproducibility’s past year of commit activity
    Jupyter Notebook 9 3 0 1 Updated Mar 10, 2026
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 144 GPL-3.0 19 13 0 Updated Mar 10, 2026
  • 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 5 4 0 Updated Mar 9, 2026
  • spatialdata-db Public
    theislab/spatialdata-db’s past year of commit activity
    Jupyter Notebook 10 BSD-3-Clause 1 26 3 Updated Mar 10, 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 27 BSD-3-Clause 2 0 2 Updated Mar 9, 2026
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