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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 946 223

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 451 108

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 390 50

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 374 61

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 365 70

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

    HTML 321 41

Repositories

Showing 10 of 234 repositories
  • multimil Public

    Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases

    theislab/multimil’s past year of commit activity
    Python 33 BSD-3-Clause 6 9 1 Updated Jul 12, 2025
  • graphcompass Public

    GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems

    theislab/graphcompass’s past year of commit activity
    Jupyter Notebook 36 MIT 1 1 2 Updated Jul 11, 2025
  • CellFlow Public

    Modeling complex perturbations with CellFlow

    theislab/CellFlow’s past year of commit activity
    Python 67 9 48 11 Updated Jul 11, 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 Jul 11, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 137 GPL-3.0 19 15 1 Updated Jul 10, 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 Jul 10, 2025
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 294 Apache-2.0 30 41 (1 issue needs help) 3 Updated Jul 10, 2025
  • sample-prediction-pipeline Public
    theislab/sample-prediction-pipeline’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Jul 10, 2025
  • DRVI Public

    Unsupervised Deep Disentangled Representation of Single-Cell Omics

    theislab/DRVI’s past year of commit activity
    Python 44 BSD-3-Clause 3 6 1 Updated Jul 10, 2025
  • ehrdata Public

    A datastructure for EHR data

    theislab/ehrdata’s past year of commit activity
    Python 7 Apache-2.0 3 16 0 Updated Jul 9, 2025
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