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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 818 162

  2. dragonn dragonn Public

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

    Jupyter Notebook 253 71

  3. atac_dnase_pipelines atac_dnase_pipelines Public

    ATAC-seq and DNase-seq processing pipeline

    Python 160 81

  4. bpnet bpnet Public

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

    Jupyter Notebook 141 33

  5. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Jupyter Notebook 121 29

  6. chrombpnet chrombpnet Public

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

    Jupyter Notebook 112 30

Repositories

Showing 10 of 167 repositories
  • 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 8 MIT 2 2 0 Updated Sep 7, 2024
  • kundajelab/DART-Eval’s past year of commit activity
    Jupyter Notebook 9 0 0 0 Updated Sep 2, 2024
  • ProCapNet Public

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

    kundajelab/ProCapNet’s past year of commit activity
    Jupyter Notebook 11 4 0 0 Updated Aug 29, 2024
  • chrombpnet Public

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

    kundajelab/chrombpnet’s past year of commit activity
    Jupyter Notebook 112 MIT 30 14 1 Updated Aug 27, 2024
  • TENet Public
    kundajelab/TENet’s past year of commit activity
    0 0 0 0 Updated Aug 12, 2024
  • kundajelab/affinity_distillation’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Aug 10, 2024
  • 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
    Jupyter Notebook 141 MIT 33 16 1 Updated Aug 2, 2024
  • kundajelab/CTCFMutants’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Jul 8, 2024
  • kundajelab/atacseq-dnaseseq-chrombpnet-modelzoo-pipeline’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated May 31, 2024
  • synapse-backup-syncer Public

    Create and sync backups to Synapse

    kundajelab/synapse-backup-syncer’s past year of commit activity
    Shell 0 0 0 0 Updated May 8, 2024