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@kundajelab

Kundaje Lab

Compbio and machine learning code repositories from the Kundaje Lab at Stanford Genetics and Computer Science Depts.

Popular repositories Loading

  1. deeplift deeplift Public

    Public facing deeplift repo

    Python 860 168

  2. dragonn dragonn Public

    A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

    Jupyter Notebook 261 71

  3. chrombpnet chrombpnet Public

    Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

    Jupyter Notebook 170 47

  4. atac_dnase_pipelines atac_dnase_pipelines Public

    ATAC-seq and DNase-seq processing pipeline

    Python 166 78

  5. bpnet bpnet Public

    Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

    Jupyter Notebook 159 34

  6. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Jupyter Notebook 144 29

Repositories

Showing 10 of 182 repositories
  • e2g-frontend Public
    kundajelab/e2g-frontend’s past year of commit activity
    JavaScript 0 Apache-2.0 0 1 1 Updated Jul 16, 2025
  • chrombpnet Public

    Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

    kundajelab/chrombpnet’s past year of commit activity
    Jupyter Notebook 170 MIT 47 7 2 Updated Jul 16, 2025
  • variant-scorer Public

    A framework to score and analyze variant effects genome-wide using ChromBPNet models

    kundajelab/variant-scorer’s past year of commit activity
    Python 13 MIT 4 2 0 Updated Jul 11, 2025
  • kundajelab/bpnet-refactor’s past year of commit activity
    Python 7 MIT 4 5 1 Updated Jul 10, 2025
  • kundajelab/chrombpnet-pytorch’s past year of commit activity
    Python 0 BSD-3-Clause 2 0 0 Updated Jul 1, 2025
  • histobpnet Public Forked from kundajelab/chrombpnet-pytorch

    Sequence to histone models

    kundajelab/histobpnet’s past year of commit activity
    Python 0 BSD-3-Clause 2 0 0 Updated Jun 25, 2025
  • v2f-frontend Public archive
    kundajelab/v2f-frontend’s past year of commit activity
    JavaScript 1 Apache-2.0 0 0 0 Updated Jun 11, 2025
  • ProCapNet Public

    Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.

    kundajelab/ProCapNet’s past year of commit activity
    Jupyter Notebook 15 2 0 0 Updated Jun 10, 2025
  • varscore Public

    Core functions for variant scoring

    kundajelab/varscore’s past year of commit activity
    Python 0 0 6 0 Updated May 29, 2025
  • kundajelab/kundajelab.github.io’s past year of commit activity
    HTML 0 MIT 0 5 0 Updated May 7, 2025