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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 988 227

  2. scvelo scvelo Public

    RNA Velocity generalized through dynamical modeling

    Python 456 110

  3. cellrank cellrank Public

    CellRank: dynamics from multi-view single-cell data

    Python 393 50

  4. scarches scarches Public

    Reference mapping for single-cell genomics

    Jupyter Notebook 377 63

  5. scib scib Public

    Benchmarking analysis of data integration tools

    Python 373 69

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

    HTML 324 40

Repositories

Showing 10 of 235 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 Aug 13, 2025
  • regvelo Public

    inferring regulatory cellular dynamics

    theislab/regvelo’s past year of commit activity
    Python 50 BSD-3-Clause 5 2 0 Updated Aug 13, 2025
  • gh-dashboard Public

    A dashboard of everything in the theislab GitHub repository

    theislab/gh-dashboard’s past year of commit activity
    HTML 6 0 2 0 Updated Aug 13, 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 6 Apache-2.0 2 4 0 Updated Aug 13, 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 Aug 13, 2025
  • hadge Public

    Comprehensive pipeline for donor demultiplexing in single cell

    theislab/hadge’s past year of commit activity
    Nextflow 24 MIT 8 11 2 Updated Aug 13, 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 Aug 12, 2025
  • ehrapy Public

    Electronic Health Record Analysis with Python.

    theislab/ehrapy’s past year of commit activity
    Python 300 Apache-2.0 34 41 (1 issue needs help) 3 Updated Aug 12, 2025
  • archmap_data Public
    theislab/archmap_data’s past year of commit activity
    Python 1 0 1 1 Updated Aug 12, 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 Aug 11, 2025
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