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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 435 79

  5. ehrapy ehrapy Public

    Electronic Health Record Analysis with Python.

    Python 369 54

  6. moscot moscot Public

    Multi-omic single-cell optimal transport tools

    Python 217 16

Repositories

Showing 10 of 277 repositories
  • sckitflow Public
    theislab/sckitflow's past year of commit activity
    Python 7 BSD-3-Clause 1 20 (1 issue needs help) 2 Updated Oct 22, 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 22, 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 22, 2026
  • cellucid-r Public

    From R to exploration in Cellucid. One function, minimal footprint.

    theislab/cellucid-r's past year of commit activity
    R 0 0 0 0 Updated Oct 21, 2026
  • 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 21, 2026
  • cellucid-demo-custom-datasets Public

    User dataset exports demo for the Cellucid web app.

    theislab/cellucid-demo-custom-datasets's past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Oct 21, 2026
  • cellucid-datasets Public

    Sample dataset exports for the Cellucid web app, hosted separately to keep the app lightweight and allow independent dataset updates.

    theislab/cellucid-datasets's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 21, 2026
  • cellucid-annotation Public template

    From clusters to consensus. Collaborative cell type annotation for Cellucid.

    theislab/cellucid-annotation's past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Oct 21, 2026
  • sprotmetrics Public

    Quality metrics for imaging-based spatial proteomics: segmentation, signal-to-background, normalization, marker distribution and technical-covariate diagnostics.

    theislab/sprotmetrics's past year of commit activity
    Python 1 MIT 0 0 1 Updated Oct 21, 2026
  • regvelo Public

    inferring regulatory cellular dynamics

    theislab/regvelo's past year of commit activity
    Python 199 BSD-3-Clause 24 0 0 Updated Oct 21, 2026
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