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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 960 222

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 452 110

  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 375 61

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 372 69

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

    HTML 321 41

Repositories

Showing 10 of 235 repositories
  • multimil_reproducibility Public
    theislab/multimil_reproducibility’s past year of commit activity
    Jupyter Notebook 6 1 4 0 Updated Jul 24, 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 Jul 24, 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 24, 2025
  • pertpy-reproducibility Public
    theislab/pertpy-reproducibility’s past year of commit activity
    Jupyter Notebook 3 Apache-2.0 2 0 0 Updated Jul 24, 2025
  • archmap_data Public
    theislab/archmap_data’s past year of commit activity
    Python 1 0 1 1 Updated Jul 23, 2025
  • scarches Public

    Reference mapping for single-cell genomics

    theislab/scarches’s past year of commit activity
    Jupyter Notebook 375 BSD-3-Clause 61 53 9 Updated Jul 23, 2025
  • anndata2ri Public

    Convert between AnnData and SingleCellExperiment

    theislab/anndata2ri’s past year of commit activity
    Python 137 GPL-3.0 19 14 1 Updated Jul 22, 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 22, 2025
  • spatial_scooby Public Forked from gagneurlab/scooby

    spatial_scooby: Modeling spatial transcriptomics from DNA sequence at single-cell resolution.

    theislab/spatial_scooby’s past year of commit activity
    Python 0 MIT 4 0 0 Updated Jul 22, 2025
  • paperbee Public
    theislab/paperbee’s past year of commit activity
    Python 54 MIT 6 5 (1 issue needs help) 7 Updated Jul 21, 2025
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