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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 805 162

  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 159 81

  4. bpnet bpnet Public

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

    Jupyter Notebook 137 32

  5. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Jupyter Notebook 119 28

  6. chipseq_pipeline chipseq_pipeline Public

    AQUAS TF and histone ChIP-seq pipeline

    Java 105 40

Repositories

Showing 10 of 166 repositories
  • kundajelab/DART-Eval’s past year of commit activity
    Jupyter Notebook 4 0 0 0 Updated Jun 24, 2024
  • 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 Jun 18, 2024
  • kundajelab/atacseq-dnaseseq-chrombpnet-modelzoo-pipeline’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated May 31, 2024
  • ProCapNet Public

    Repository for modeling PRO-cap data with BPNet.

    kundajelab/ProCapNet’s past year of commit activity
    Jupyter Notebook 8 2 0 0 Updated May 21, 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
  • kundajelab/anvil-variant-scoring’s past year of commit activity
    WDL 0 0 0 0 Updated May 7, 2024
  • kundajelab/bpnet-refactor’s past year of commit activity
    Python 3 MIT 0 5 1 Updated Apr 7, 2024
  • chrombpnet Public

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

    kundajelab/chrombpnet’s past year of commit activity
    Jupyter Notebook 102 MIT 25 8 1 Updated Jan 29, 2024
  • tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    kundajelab/tfmodisco’s past year of commit activity
    Jupyter Notebook 119 MIT 28 19 4 Updated Jan 28, 2024
  • scATAC-reprog Public

    Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency" by Nair, Ameen et al.

    kundajelab/scATAC-reprog’s past year of commit activity
    Jupyter Notebook 6 1 0 0 Updated Jan 9, 2024

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