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 882 167

  2. dragonn dragonn Public

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

    Jupyter Notebook 264 66

  3. chrombpnet chrombpnet Public

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

    Jupyter Notebook 256 68

  4. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Python 193 39

  5. bpnet bpnet Public

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

    Python 187 39

  6. atac_dnase_pipelines atac_dnase_pipelines Public

    ATAC-seq and DNase-seq processing pipeline

    Python 166 78

Repositories

Showing 10 of 194 repositories
  • igvf_pseudobulking_pipeline Public

    Code for assisting with pseudobulking IGVF single cell data.

    kundajelab/igvf_pseudobulking_pipeline's past year of commit activity
    Python 2 1 0 0 Updated Oct 5, 2026
  • ProCapNet Public

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

    kundajelab/ProCapNet's past year of commit activity
    Jupyter Notebook 22 MIT 5 0 0 Updated Oct 4, 2026
  • tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    kundajelab/tfmodisco's past year of commit activity
    Python 193 MIT 39 6 3 Updated Oct 1, 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 Sep 30, 2026
  • varscore Public

    Core functions for variant scoring

    kundajelab/varscore's past year of commit activity
    Python 2 1 4 0 Updated Sep 18, 2026
  • kundajelab/MotifCompendium's past year of commit activity
    HTML 16 MIT 3 0 1 Updated Sep 15, 2026
  • kundajelab/kundajelab.github.io's past year of commit activity
    HTML 0 MIT 0 4 1 Updated Sep 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 Sep 4, 2026
  • Fi-NeMo Public

    Identifying transcription factor binding sites from neural network contribution scores

    kundajelab/Fi-NeMo's past year of commit activity
    Python 27 MIT 1 0 2 Updated Aug 26, 2026
  • ucsc-trackhub-encode.github.io Public

    UCSC Track Hub for ENCODE BPNet family models

    kundajelab/ucsc-trackhub-encode.github.io's past year of commit activity
    HTML 0 0 0 0 Updated Aug 15, 2026