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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 881 166

  2. chrombpnet chrombpnet Public

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

    Jupyter Notebook 266 70

  3. dragonn dragonn Public

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

    Jupyter Notebook 264 66

  4. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Python 200 43

  5. bpnet bpnet Public

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

    Python 188 38

  6. atac_dnase_pipelines atac_dnase_pipelines Public

    ATAC-seq and DNase-seq processing pipeline

    Python 166 78

Repositories

Showing 10 of 200 repositories
  • genesis-preprocessing Public

    Folder for preprocessing plant omics data before model training

    kundajelab/genesis-preprocessing's past year of commit activity
    Python 2 1 0 0 Updated Nov 13, 2026
  • bpnet-refactor Public
    kundajelab/bpnet-refactor's past year of commit activity
    Python 9 MIT 5 5 2 Updated Nov 12, 2026
  • chrombpnet-refactor Public

    A refactored version of ChromBPNet in PyTorch/TensorFlow/JAX: A Bias factorized, base-resolution deep learning models of chromatin accessibility

    kundajelab/chrombpnet-refactor's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Nov 11, 2026
  • MotifCompendium Public
    kundajelab/MotifCompendium's past year of commit activity
    HTML 18 MIT 3 0 1 Updated Nov 11, 2026
  • deeplift-extension-repro Public

    Code to reproduce figures and results in the deeplift-extension paper

    kundajelab/deeplift-extension-repro's past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Nov 11, 2026
  • Fi-NeMo Public

    Identifying transcription factor binding sites from neural network contribution scores

    kundajelab/Fi-NeMo's past year of commit activity
    Python 29 MIT 1 0 2 Updated Nov 10, 2026
  • TranscriptML Public

    Training and interpreting RNA sequence-to-function models

    kundajelab/TranscriptML's past year of commit activity
    Python 1 MIT 0 0 0 Updated Nov 10, 2026
  • tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    kundajelab/tfmodisco's past year of commit activity
    Python 200 MIT 43 6 5 Updated Nov 5, 2026
  • procap-atlas Public

    Preprocessing and deep learning-based analysis of the ENCODE PRO-cap atlas

    kundajelab/procap-atlas's past year of commit activity
    Python 1 MIT 0 0 0 Updated Nov 5, 2026
  • SMFNet Public

    Official implementation of SMFNet, a discrete diffusion model of single-molecule footprinting reads

    kundajelab/SMFNet's past year of commit activity
    Python 5 MIT 1 0 0 Updated Nov 5, 2026
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