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    • Fi-NeMo

      Public
      Identifying transcription factor binding sites from neural network contribution scores
      Python
      01202Updated Nov 1, 2025Nov 1, 2025
    • igvf_pseudobulking_pipeline

      Public
      Code for assisting with pseudobulking IGVF single cell data.
      Python
      1000Updated Oct 24, 2025Oct 24, 2025
    • shap

      Public
      A unified approach to explain the output of any machine learning model.
      Jupyter Notebook
      3.4k1001Updated Oct 23, 2025Oct 23, 2025
    • IGVF_helpers

      Public
      Scripts to help with IGVF single cell processing
      Python
      0000Updated Oct 21, 2025Oct 21, 2025
    • chrombpnet-pytorch

      Public
      Python
      7000Updated Oct 20, 2025Oct 20, 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 fibroblast reprogramming to pluripotency" by Nair, Ameen et al.
      Jupyter Notebook
      11110Updated Oct 16, 2025Oct 16, 2025
    • varscore

      Public
      Core functions for variant scoring
      Python
      0160Updated Oct 15, 2025Oct 15, 2025
    • gp_mouse

      Public
      Jupyter Notebook
      0000Updated Oct 13, 2025Oct 13, 2025
    • tfmodisco

      Public
      TF MOtif Discovery from Importance SCOres
      Python
      3215502Updated Oct 12, 2025Oct 12, 2025
    • bpnet

      Public
      Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
      Python
      3616800Updated Oct 10, 2025Oct 10, 2025
    • histobpnet

      Public
      Sequence to histone models
      Python
      7000Updated Oct 7, 2025Oct 7, 2025
    • MotifCompendium

      Public
      HTML
      0600Updated Sep 25, 2025Sep 25, 2025
    • bpnet-refactor

      Public
      Python
      4951Updated Sep 22, 2025Sep 22, 2025
    • Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
      Jupyter Notebook
      48185193Updated Sep 11, 2025Sep 11, 2025
    • ProCapNet

      Public
      Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
      Jupyter Notebook
      31500Updated Aug 28, 2025Aug 28, 2025
    • e2g-frontend

      Public
      TypeScript
      0200Updated Aug 20, 2025Aug 20, 2025
    • variant-scorer

      Public
      A framework to score and analyze variant effects genome-wide using ChromBPNet models
      Python
      51620Updated Aug 1, 2025Aug 1, 2025
    • HTML
      0050Updated Jul 26, 2025Jul 26, 2025
    • DART-Eval

      Public
      Jupyter Notebook
      54230Updated Jul 24, 2025Jul 24, 2025
    • v2f-frontend

      Public archive
      JavaScript
      0100Updated Jun 11, 2025Jun 11, 2025
    • archive

      Public
      HTML
      0000Updated May 5, 2025May 5, 2025
    • bam2bw

      Public
      A command-line tool for reading SAM/BAM files and converted them directly to bigwig files.
      Python
      3000Updated May 1, 2025May 1, 2025
    • CLIP-based model for aligning epitopes to immune receptors
      Python
      11100Updated Apr 30, 2025Apr 30, 2025
    • A framework to score and analyze variant effects genome-wide using ProCapNet models
      Python
      5000Updated Apr 1, 2025Apr 1, 2025
    • 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
      0200Updated Feb 19, 2025Feb 19, 2025
    • Designing AAV sequences for retinal cell types (with scATAC-seq models)
      Jupyter Notebook
      0100Updated Feb 17, 2025Feb 17, 2025
    • Official Kundaje Lab Blog
      HTML
      0002Updated Jan 31, 2025Jan 31, 2025
    • A library for common variant scoring operations
      0000Updated Jan 17, 2025Jan 17, 2025
    • Jupyter Notebook
      0200Updated Jan 10, 2025Jan 10, 2025
    • A method for analyzing scATAC-seq experiments.
      Python
      9000Updated Sep 30, 2024Sep 30, 2024