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@kundajelab

Kundaje Lab

Compbio and machine learning code repositories from the Kundaje Lab at Stanford Genetics and Computer Science Depts.

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  1. deeplift deeplift Public

    Public facing deeplift repo

    Python 829 164

  2. dragonn dragonn Public

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

    Jupyter Notebook 256 71

  3. atac_dnase_pipelines atac_dnase_pipelines Public

    ATAC-seq and DNase-seq processing pipeline

    Python 162 81

  4. bpnet bpnet Public

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

    Jupyter Notebook 142 35

  5. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Jupyter Notebook 124 29

  6. chrombpnet chrombpnet Public

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

    Jupyter Notebook 124 34

Repositories

Showing 10 of 169 repositories
  • 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 7 MIT 1 0 0 Updated Nov 12, 2024
  • retina-design Public

    Designing AAV sequences for retinal cell types (with scATAC-seq models)

    kundajelab/retina-design’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Nov 10, 2024
  • kundajelab/DART-Eval’s past year of commit activity
    Jupyter Notebook 17 1 1 0 Updated Nov 6, 2024
  • ImmuneCLIP Public

    Repository for code and data related to ImmuneCLIP

    kundajelab/ImmuneCLIP’s past year of commit activity
    Python 5 MIT 1 0 0 Updated Nov 1, 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 Oct 30, 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 12 4 0 0 Updated Oct 3, 2024
  • TENet Public
    kundajelab/TENet’s past year of commit activity
    Python 1 0 0 0 Updated Sep 22, 2024
  • chrombpnet Public

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

    kundajelab/chrombpnet’s past year of commit activity
    Jupyter Notebook 124 MIT 34 12 1 Updated Aug 27, 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 142 MIT 35 16 1 Updated Aug 2, 2024

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