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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 850 166

  2. dragonn dragonn Public

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

    Jupyter Notebook 259 71

  3. atac_dnase_pipelines atac_dnase_pipelines Public

    ATAC-seq and DNase-seq processing pipeline

    Python 165 79

  4. bpnet bpnet Public

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

    Jupyter Notebook 150 34

  5. chrombpnet chrombpnet Public

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

    Jupyter Notebook 141 36

  6. tfmodisco tfmodisco Public

    TF MOtif Discovery from Importance SCOres

    Jupyter Notebook 133 29

Repositories

Showing 10 of 176 repositories
  • kundajelab/kundajelab.github.io’s past year of commit activity
    HTML 0 MIT 0 5 1 Updated Feb 22, 2025
  • neuro-variants Public

    This repository contains all scripts for the manuscript "Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart" by Marderstein, Kundu et al.

    kundajelab/neuro-variants’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Feb 19, 2025
  • ImmuneCLIP Public

    CLIP-based model for aligning epitopes to immune receptors

    kundajelab/ImmuneCLIP’s past year of commit activity
    Python 7 MIT 0 0 0 Updated Feb 18, 2025
  • 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 MIT 0 0 0 Updated Feb 17, 2025
  • varscore Public

    Core functions for variant scoring

    kundajelab/varscore’s past year of commit activity
    Python 0 0 2 0 Updated Feb 17, 2025
  • 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 9 MIT 3 3 0 Updated Feb 17, 2025
  • kundajelab/bpnet-refactor’s past year of commit activity
    Python 4 MIT 0 5 1 Updated Feb 13, 2025
  • v2f-frontend Public
    kundajelab/v2f-frontend’s past year of commit activity
    JavaScript 0 Apache-2.0 0 12 1 Updated Feb 10, 2025
  • chrombpnet Public

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

    kundajelab/chrombpnet’s past year of commit activity
    Jupyter Notebook 141 MIT 36 6 1 Updated Feb 7, 2025
  • kundajelab_old.github.io Public

    Official Kundaje Lab Blog

    kundajelab/kundajelab_old.github.io’s past year of commit activity
    HTML 0 0 0 2 Updated Jan 31, 2025

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