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    176 repositories

    • DART-Eval

      Public
      Jupyter Notebook
      •1•27•1•0•Updated Feb 27, 2025Feb 27, 2025

    • kundajelab.github.io

      Public
      HTML
      •
      MIT License
      •0•0•5•0•Updated Feb 27, 2025Feb 27, 2025

    • varscore

      Public
      Core functions for variant scoring
      Python
      •0•0•2•0•Updated Feb 27, 2025Feb 27, 2025

    • bpnet-refactor

      Public
      Python
      •
      MIT License
      •1•4•3•1•Updated Feb 25, 2025Feb 25, 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.
      Jupyter Notebook
      •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

    • ImmuneCLIP

      Public
      CLIP-based model for aligning epitopes to immune receptors
      Python
      •
      MIT License
      •0•8•1•0•Updated Feb 18, 2025Feb 18, 2025

    • retina-design

      Public
      Designing AAV sequences for retinal cell types (with scATAC-seq models)
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Feb 17, 2025Feb 17, 2025

    • variant-scorer

      Public
      A framework to score and analyze variant effects genome-wide using ChromBPNet models
      Python
      •
      MIT License
      •3•9•3•0•Updated Feb 17, 2025Feb 17, 2025

    • v2f-frontend

      Public
      JavaScript
      •
      Apache License 2.0
      •0•0•12•1•Updated Feb 10, 2025Feb 10, 2025

    • chrombpnet

      Public
      Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
      Jupyter Notebook
      •
      MIT License
      •38•143•6•1•Updated Feb 7, 2025Feb 7, 2025

    • kundajelab_old.github.io

      Public
      Official Kundaje Lab Blog
      HTML
      •0•0•0•2•Updated Jan 31, 2025Jan 31, 2025

    • varscore-old

      Public
      A library for common variant scoring operations
      0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • chrombpnet-figures

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • ProCapNet

      Public
      Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
      Jupyter Notebook
      •3•13•0•0•Updated Dec 27, 2024Dec 27, 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.
      Jupyter Notebook
      •
      MIT License
      •1•10•0•0•Updated Nov 12, 2024Nov 12, 2024

    • dragonnfruit

      Public
      A method for analyzing scATAC-seq experiments.
      Python
      •
      MIT License
      •10•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • TENet

      Public
      Python
      •0•1•0•0•Updated Sep 22, 2024Sep 22, 2024

    • affinity_distillation

      Public
      Jupyter Notebook
      •1•1•1•0•Updated Aug 10, 2024Aug 10, 2024

    • bpnet

      Public
      Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
      Jupyter Notebook
      •
      MIT License
      •34•151•18•1•Updated Aug 2, 2024Aug 2, 2024

    • CTCFMutants

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jul 8, 2024Jul 8, 2024

    • atacseq-dnaseseq-chrombpnet-modelzoo-pipeline

      Public
      Jupyter Notebook
      •1•0•0•0•Updated May 31, 2024May 31, 2024

    • synapse-backup-syncer

      Public
      Create and sync backups to Synapse
      Shell
      •0•0•0•0•Updated May 8, 2024May 8, 2024

    • anvil-variant-scoring

      Public
      WDL
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • tfmodisco

      Public
      TF MOtif Discovery from Importance SCOres
      Jupyter Notebook
      •
      MIT License
      •29•134•22•4•Updated Jan 28, 2024Jan 28, 2024

    • encode_upload_tfatlas_readmes

      Public
      0•0•0•0•Updated Aug 21, 2023Aug 21, 2023

    • Cardiogenesis_Repo

      Public
      Cardiogenesis Repo
      Jupyter Notebook
      •2•9•0•0•Updated Aug 8, 2023Aug 8, 2023

    • dragonn

      Public
      A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
      deep-learninggenomics
      Jupyter Notebook
      •
      MIT License
      •71•259•15•2•Updated Aug 1, 2023Aug 1, 2023

    • hitcallerNet

      Public
      0•0•0•0•Updated May 25, 2023May 25, 2023

    • track-hubs

      Public
      Python
      •0•0•0•0•Updated Apr 1, 2023Apr 1, 2023

    • ENCODE_manual_liver

      Public
      Python
      •1•0•0•0•Updated Mar 31, 2023Mar 31, 2023