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    187 repositories

    • Fi-NeMo

      Public
      Identifying transcription factor binding sites from neural network contribution scores
      Python
      •
      MIT License
      •0•12•0•2•Updated Nov 1, 2025Nov 1, 2025

    • igvf_pseudobulking_pipeline

      Public
      Code for assisting with pseudobulking IGVF single cell data.
      Python
      •1•0•0•0•Updated Oct 24, 2025Oct 24, 2025

    • shap

      Public
      A unified approach to explain the output of any machine learning model.
      Jupyter Notebook
      •
      MIT License
      •3.4k•10•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

    • chrombpnet-pytorch

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•0•0•0•Updated 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
      •
      MIT License
      •1•11•1•0•Updated Oct 16, 2025Oct 16, 2025

    • varscore

      Public
      Core functions for variant scoring
      Python
      •0•1•6•0•Updated Oct 15, 2025Oct 15, 2025

    • gp_mouse

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • tfmodisco

      Public
      TF MOtif Discovery from Importance SCOres
      Python
      •
      MIT License
      •32•155•0•2•Updated Oct 12, 2025Oct 12, 2025

    • bpnet

      Public
      Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
      Python
      •
      MIT License
      •36•168•0•0•Updated Oct 10, 2025Oct 10, 2025

    • histobpnet

      Public
      Sequence to histone models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•0•0•0•Updated Oct 7, 2025Oct 7, 2025

    • MotifCompendium

      Public
      HTML
      •
      MIT License
      •0•6•0•0•Updated Sep 25, 2025Sep 25, 2025

    • bpnet-refactor

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

    • chrombpnet

      Public
      Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
      Jupyter Notebook
      •
      MIT License
      •48•185•19•3•Updated Sep 11, 2025Sep 11, 2025

    • ProCapNet

      Public
      Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
      Jupyter Notebook
      •
      MIT License
      •3•15•0•0•Updated Aug 28, 2025Aug 28, 2025

    • e2g-frontend

      Public
      TypeScript
      •
      Apache License 2.0
      •0•2•0•0•Updated Aug 20, 2025Aug 20, 2025

    • variant-scorer

      Public
      A framework to score and analyze variant effects genome-wide using ChromBPNet models
      Python
      •
      MIT License
      •5•16•2•0•Updated Aug 1, 2025Aug 1, 2025

    • kundajelab.github.io

      Public
      HTML
      •
      MIT License
      •0•0•5•0•Updated Jul 26, 2025Jul 26, 2025

    • DART-Eval

      Public
      Jupyter Notebook
      •5•42•3•0•Updated Jul 24, 2025Jul 24, 2025

    • v2f-frontend

      Public archive
      JavaScript
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 11, 2025Jun 11, 2025

    • archive

      Public
      HTML
      •0•0•0•0•Updated May 5, 2025May 5, 2025

    • bam2bw

      Public
      A command-line tool for reading SAM/BAM files and converted them directly to bigwig files.
      Python
      •
      MIT License
      •3•0•0•0•Updated May 1, 2025May 1, 2025

    • ImmuneCLIP

      Public
      CLIP-based model for aligning epitopes to immune receptors
      Python
      •
      MIT License
      •1•11•0•0•Updated Apr 30, 2025Apr 30, 2025

    • variant-scorer-procapnet

      Public
      A framework to score and analyze variant effects genome-wide using ProCapNet models
      Python
      •
      MIT License
      •5•0•0•0•Updated Apr 1, 2025Apr 1, 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•2•0•0•Updated Feb 19, 2025Feb 19, 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

    • 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•2•0•0•Updated Jan 10, 2025Jan 10, 2025

    • dragonnfruit

      Public
      A method for analyzing scATAC-seq experiments.
      Python
      •
      MIT License
      •9•0•0•0•Updated Sep 30, 2024Sep 30, 2024