Skip to content
@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 864 168

  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 177 48

  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 162 36

  6. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Jupyter Notebook 146 29

Repositories

Showing 10 of 182 repositories
  • histobpnet Public Forked from kundajelab/chrombpnet-pytorch

    Sequence to histone models

    kundajelab/histobpnet’s past year of commit activity
    Python 0 BSD-3-Clause 5 0 0 Updated Sep 5, 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 MIT 2 0 0 Updated Aug 28, 2025
  • e2g-frontend Public
    kundajelab/e2g-frontend’s past year of commit activity
    TypeScript 0 Apache-2.0 0 0 0 Updated Aug 20, 2025
  • kundajelab/chrombpnet-pytorch’s past year of commit activity
    Python 0 BSD-3-Clause 5 0 0 Updated Aug 13, 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 14 MIT 4 1 0 Updated Aug 1, 2025
  • varscore Public

    Core functions for variant scoring

    kundajelab/varscore’s past year of commit activity
    Python 0 0 6 0 Updated Jul 31, 2025
  • kundajelab/kundajelab.github.io’s past year of commit activity
    HTML 0 MIT 0 5 0 Updated Jul 26, 2025
  • DART-Eval Public
    kundajelab/DART-Eval’s past year of commit activity
    Jupyter Notebook 41 4 4 0 Updated Jul 24, 2025
  • chrombpnet Public

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

    kundajelab/chrombpnet’s past year of commit activity
    Jupyter Notebook 177 MIT 48 11 2 Updated Jul 16, 2025
  • kundajelab/bpnet-refactor’s past year of commit activity
    Python 8 MIT 4 5 1 Updated Jul 10, 2025