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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 881 166

  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 260 68

  4. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Python 198 42

  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 196 repositories
  • genesis-curation Public

    Genesis metadata curation, review, records, studies and method benchmarks

    kundajelab/genesis-curation's past year of commit activity
    Python 0 0 0 0 Updated Oct 29, 2026
  • 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 3 Updated Oct 29, 2026
  • chrombpnet Public

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

    kundajelab/chrombpnet's past year of commit activity
    Jupyter Notebook 260 MIT 68 31 4 Updated Oct 29, 2026
  • 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 28, 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 Oct 24, 2026
  • kundajelab/MotifCompendium's past year of commit activity
    HTML 17 MIT 3 0 1 Updated Oct 22, 2026
  • tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    kundajelab/tfmodisco's past year of commit activity
    Python 198 MIT 42 6 5 Updated Oct 16, 2026
  • kundajelab/kundajelab.github.io's past year of commit activity
    HTML 0 MIT 0 4 1 Updated Oct 12, 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 Oct 7, 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 23 MIT 5 0 0 Updated Oct 4, 2026