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 865 168

  2. dragonn dragonn Public

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

    Jupyter Notebook 262 68

  3. chrombpnet chrombpnet Public

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

    Jupyter Notebook 179 46

  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

    Python 166 36

  6. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Python 148 30

Repositories

Showing 10 of 184 repositories
  • tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    kundajelab/tfmodisco’s past year of commit activity
    Python 148 MIT 30 0 0 Updated Oct 2, 2025
  • bpnet Public

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

    kundajelab/bpnet’s past year of commit activity
    Python 166 MIT 36 0 0 Updated Sep 26, 2025
  • kundajelab/MotifCompendium’s past year of commit activity
    HTML 6 MIT 0 0 0 Updated Sep 24, 2025
  • Fi-NeMo Public Forked from austintwang/finemo_gpu

    Identifying transcription factor binding sites from neural network contribution scores

    kundajelab/Fi-NeMo’s past year of commit activity
    Python 5 MIT 3 0 0 Updated Sep 24, 2025
  • kundajelab/bpnet-refactor’s past year of commit activity
    Python 8 MIT 4 5 1 Updated Sep 22, 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 6 0 0 Updated Sep 18, 2025
  • varscore Public

    Core functions for variant scoring

    kundajelab/varscore’s past year of commit activity
    Python 0 0 6 0 Updated Sep 13, 2025
  • chrombpnet Public

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

    kundajelab/chrombpnet’s past year of commit activity
    Jupyter Notebook 179 MIT 47 13 3 Updated Sep 10, 2025
  • kundajelab/chrombpnet-pytorch’s past year of commit activity
    Python 0 BSD-3-Clause 6 0 0 Updated Sep 10, 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 3 0 0 Updated Aug 28, 2025