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@theislab

Theis Lab

Institute of Computational Biology

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  1. single-cell-best-practices single-cell-best-practices Public

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

    Jupyter Notebook 934 219

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 448 106

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 389 50

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 371 60

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 363 69

  6. single-cell-transformer-papers single-cell-transformer-papers Public

    HTML 320 41

Repositories

Showing 10 of 233 repositories
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 294 Apache-2.0 28 42 (1 issue needs help) 3 Updated Jun 26, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 5 Apache-2.0 3 18 2 Updated Jun 26, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 57 7 47 12 Updated Jun 26, 2025
  • ehrapy-datasets Public

    A collection of scripts to generate AnnData objects of EHR datasets for ehrapy

    theislab/ehrapy-datasets’s past year of commit activity
    Jupyter Notebook 7 Apache-2.0 2 2 0 Updated Jun 26, 2025
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 5 0 0 0 Updated Jun 26, 2025
  • txsim Public
    theislab/txsim’s past year of commit activity
    Python 3 2 36 4 Updated Jun 26, 2025
  • FlatVI Public
    theislab/FlatVI’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated Jun 25, 2025
  • troutpy Public

    Package for the analysis of Transcripts outside segmented cells in ST data

    theislab/troutpy’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 1 Updated Jun 25, 2025
  • CFGen Public
    theislab/CFGen’s past year of commit activity
    Jupyter Notebook 17 MIT 5 0 0 Updated Jun 25, 2025
  • 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 6 2 0 Updated Jun 24, 2025
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