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@kundajelab Kundaje Lab

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    194 repositories

    • procap-atlas

      Public
      Preprocessing and deep learning-based analysis of the ENCODE PRO-cap atlas
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 15, 2026Sep 15, 2026

    • MotifCompendium

      Public
      HTML
      •
      MIT License
      •3•14•0•1•Updated Sep 15, 2026Sep 15, 2026

    • varscore

      Public
      Core functions for variant scoring
      Python
      •1•2•4•2•Updated Sep 11, 2026Sep 11, 2026

    • kundajelab.github.io

      Public
      HTML
      •
      MIT License
      •0•0•4•1•Updated Sep 10, 2026Sep 10, 2026

    • igvf_pseudobulking_pipeline

      Public
      Code for assisting with pseudobulking IGVF single cell data.
      Python
      •1•2•0•0•Updated Sep 9, 2026Sep 9, 2026

    • TranscriptML

      Public
      Training and interpreting RNA sequence-to-function models
      deep-learningrnamodel-interpretation
      deep-learningrnamodel-interpretation
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 4, 2026Sep 4, 2026

    • tfmodisco

      Public
      TF MOtif Discovery from Importance SCOres
      Python
      •
      MIT License
      •39•190•6•3•Updated Sep 4, 2026Sep 4, 2026

    • Fi-NeMo

      Public
      Identifying transcription factor binding sites from neural network contribution scores
      Python
      •
      MIT License
      •1•25•0•2•Updated Aug 26, 2026Aug 26, 2026

    • ucsc-trackhub-encode.github.io

      Public
      UCSC Track Hub for ENCODE BPNet family models
      HTML
      •0•0•0•0•Updated Aug 15, 2026Aug 15, 2026

    • reporterNet

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 3, 2026Aug 3, 2026

    • e2g-frontend

      Public
      TypeScript
      •
      Apache License 2.0
      •0•2•0•0•Updated Jul 16, 2026Jul 16, 2026

    • ENCODE_atlas_bpnet_model_family_files

      Public
      Machine-readable index of downloadable ENCODE-portal files for the Kundaje-lab ENCODE Atlas BPNet-family models (BPNet / ChromBPNet / ProCapNet / ReporterNet): …
      Python
      •0•0•0•0•Updated Jul 9, 2026Jul 9, 2026

    • regulatory_lm

      Public
      The official repository for the ARSENAL model
      Python
      •0•20•0•1•Updated Jul 3, 2026Jul 3, 2026

    • chrombpnet

      Public
      Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
      Jupyter Notebook
      •
      MIT License
      •68•250•31•3•Updated Jun 9, 2026Jun 9, 2026

    • TENet

      Public
      Python
      •0•1•0•0•Updated May 11, 2026May 11, 2026

    • MPRA-DragoNN

      Public
      Code accompanying the paper "Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assa…
      Python
      •
      MIT License
      •6•13•0•1•Updated May 9, 2026May 9, 2026

    • tangermeme

      Public
      Biological sequence analysis for the modern age.
      Python
      •
      MIT License
      •34•0•0•0•Updated Apr 28, 2026Apr 28, 2026

    • 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…
      Jupyter Notebook
      •
      MIT License
      •1•7•0•0•Updated Apr 27, 2026Apr 27, 2026

    • DART-Eval

      Public
      Jupyter Notebook
      •6•52•4•0•Updated Mar 22, 2026Mar 22, 2026

    • bpnet

      Public
      Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
      Python
      •
      MIT License
      •39•185•0•0•Updated Mar 19, 2026Mar 19, 2026

    • chrombpnet-pytorch

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•1•0•0•Updated Mar 2, 2026Mar 2, 2026

    • variant-scorer

      Public
      A framework to score and analyze variant effects genome-wide using ChromBPNet models
      Python
      •
      MIT License
      •6•21•2•1•Updated Mar 2, 2026Mar 2, 2026

    • klf_smf

      Public
      Paper on KLF SMF with the Will Greenleaf lab
      Jupyter Notebook
      •0•0•0•0•Updated Feb 14, 2026Feb 14, 2026

    • gp_mouse

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • shap

      Public
      A unified approach to explain the output of any machine learning model.
      Jupyter Notebook
      •
      MIT License
      •3.8k•11•0•1•Updated Oct 23, 2025Oct 23, 2025

    • IGVF_helpers

      Public
      Scripts to help with IGVF single cell processing
      Python
      •0•0•0•0•Updated Oct 21, 2025Oct 21, 2025

    • scATAC-reprog

      Public
      Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibro…
      Jupyter Notebook
      •
      MIT License
      •2•15•1•0•Updated Oct 16, 2025Oct 16, 2025

    • bpnet-refactor

      Public
      Python
      •
      MIT License
      •4•9•5•1•Updated Sep 22, 2025Sep 22, 2025

    • ProCapNet

      Public
      Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
      Jupyter Notebook
      •
      MIT License
      •5•22•0•0•Updated Aug 28, 2025Aug 28, 2025

    • hubmaker

      Public
      A utility to programmatically make trackhub JSON files for a genome browser.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 14, 2025Jul 14, 2025
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