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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
  • single-cell-best-practices Public

    https://www.sc-best-practices.org

    theislab/single-cell-best-practices's past year of commit activity
    Jupyter Notebook 1,285 279 3 2 Updated Oct 19, 2026
  • cellink Public

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

    theislab/cellink's past year of commit activity
    Python 23 Apache-2.0 6 5 3 Updated Oct 19, 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 0 MIT 0 0 1 Updated Oct 19, 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 19, 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 19, 2026
  • cellucid Public

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

    theislab/cellucid's past year of commit activity
    JavaScript 6 BSD-3-Clause 0 0 0 Updated Oct 19, 2026
  • sckitflow Public
    theislab/sckitflow's past year of commit activity
    Python 7 BSD-3-Clause 1 27 (2 issues need help) 3 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
  • DRVI Public

    Unsupervised Deep Disentangled Representation of Single-Cell Omics

    theislab/DRVI's past year of commit activity
    Python 83 BSD-3-Clause 6 5 3 Updated Oct 19, 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 19, 2026
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