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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 279

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 512 114

  3. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 408 72

  4. scib scib Public

    Benchmarking analysis of data integration tools

    Python 429 77

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 361 53

  6. moscot moscot Public

    Multi-omic single-cell optimal transport tools

    Python 216 16

Repositories

Showing 10 of 273 repositories
  • interscale Public

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

    theislab/interscale's past year of commit activity
    Python 12 BSD-3-Clause 1 8 2 Updated Sep 8, 2026
  • sckitflow Public
    theislab/sckitflow's past year of commit activity
    Python 7 BSD-3-Clause 0 25 (2 issues need help) 5 Updated Sep 8, 2026
  • scConcept Public

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

    theislab/scConcept's past year of commit activity
    Python 38 MIT 7 2 1 Updated Sep 8, 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 Sep 8, 2026
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy's past year of commit activity
    Python 361 Apache-2.0 53 17 4 Updated Sep 8, 2026
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri's past year of commit activity
    Python 152 GPL-3.0 19 11 0 Updated Sep 8, 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 Sep 8, 2026
  • multigrate Public

    Multigrate: multiomic data integration for single-cell genomics

    theislab/multigrate's past year of commit activity
    Python 35 BSD-3-Clause 8 2 2 Updated Sep 7, 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 Sep 7, 2026
  • spatialdata-db Public
    theislab/spatialdata-db's past year of commit activity
    Jupyter Notebook 12 BSD-3-Clause 1 26 3 Updated Sep 7, 2026
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