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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 1.3k 277

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 512 117

  3. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 412 73

  4. scib scib Public

    Benchmarking analysis of data integration tools

    Python 432 78

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 366 53

  6. moscot moscot Public

    Multi-omic single-cell optimal transport tools

    Python 216 16

Repositories

Showing 10 of 274 repositories
  • donordata Public

    Single-cell experiments measure cells but are designed around donors: patients, samples, guides, compounds. DonorData keeps these levels together in one object and aligned under every operation.

    theislab/donordata's past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Oct 6, 2026
  • cellink Public

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

    theislab/cellink's past year of commit activity
    Python 21 Apache-2.0 6 5 4 Updated Oct 6, 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 1,278 277 4 1 Updated Oct 6, 2026
  • ReconEval Public

    Benchmarking for gene expression from single cell latent representations

    theislab/ReconEval's past year of commit activity
    Jupyter Notebook 21 MIT 3 1 0 Updated Oct 6, 2026
  • spatialdata-db-client Public
    theislab/spatialdata-db-client's past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Oct 6, 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 Oct 6, 2026
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri's past year of commit activity
    Python 154 GPL-3.0 19 11 0 Updated Oct 6, 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 3 0 Updated Oct 6, 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 31 BSD-3-Clause 2 0 2 Updated Oct 5, 2026
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate's past year of commit activity
    Python 35 BSD-3-Clause 9 2 2 Updated Oct 5, 2026
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