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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 513 117

  3. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 414 73

  4. scib scib Public

    Benchmarking analysis of data integration tools

    Python 434 79

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 368 54

  6. moscot moscot Public

    Multi-omic single-cell optimal transport tools

    Python 217 16

Repositories

Showing 10 of 277 repositories
  • cellucid-python Public

    The complete Python toolkit for Cellucid. Serve, export, document, explore.

    theislab/cellucid-python's past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Oct 19, 2026
  • cellucid Public

    See every cell. Query any gene. Fly through millions. Zero friction.

    theislab/cellucid's past year of commit activity
    JavaScript 7 BSD-3-Clause 0 0 0 Updated Oct 19, 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 0 0 Updated Oct 19, 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 19, 2026
  • spapros Public

    Python package for Probe set selection for targeted spatial transcriptomics.

    theislab/spapros's past year of commit activity
    Python 51 MIT 10 10 10 Updated Oct 19, 2026
  • sckitflow Public
    theislab/sckitflow's past year of commit activity
    Python 7 BSD-3-Clause 1 21 (3 issues need help) 0 Updated Oct 19, 2026
  • moscot Public

    Multi-omic single-cell optimal transport tools

    theislab/moscot's past year of commit activity
    Python 217 BSD-3-Clause 16 32 5 Updated Oct 19, 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 19, 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 32 BSD-3-Clause 2 0 2 Updated Oct 19, 2026
  • mapqc Public

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

    theislab/mapqc's past year of commit activity
    Python 12 MIT 1 0 2 Updated Oct 19, 2026
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