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    42 repositories

    • chexmix

      Public
      ChExMix: the ChIP-exo mixture model
      Java
      •
      MIT License
      •0•7•5•0•Updated Oct 24, 2025Oct 24, 2025

    • TPCAV

      Public
      Testing with PCA projected Concept Activation Vectors
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • pegr

      Public
      Platform for Eukaryotic Genome Regulation
      Groovy
      •
      MIT License
      •1•3•33•0•Updated Oct 13, 2025Oct 13, 2025

    • seqchromloader

      Public
      Provide ready-to-use dataloader for deep learning models
      Python
      •0•3•0•0•Updated Oct 9, 2025Oct 9, 2025

    • seqcode-core

      Public
      SeqCode: Java code for the analysis of high-throughput sequencing data
      Java
      •
      MIT License
      •4•6•0•0•Updated Jul 18, 2025Jul 18, 2025

    • pfal-chrom-states-trackhub

      Public
      Plasmodium falciparum chromatin state trackhubs for UCSC genome browser
      Python
      •
      MIT License
      •0•0•0•0•Updated May 23, 2025May 23, 2025

    • allo

      Public
      Allo: a multi-mapped read rescue strategy for gene regulatory analyses
      Python
      •
      MIT License
      •4•24•2•0•Updated Sep 5, 2024Sep 5, 2024

    • miniMDS

      Public
      Python
      •
      MIT License
      •9•30•5•0•Updated Jun 30, 2024Jun 30, 2024

    • Micro-C-Pipelines

      Public
      This repository contains pipelines developed for processing Micro-C data
      Python
      •1•2•0•0•Updated Jun 15, 2024Jun 15, 2024

    • Bichrom-GAT-Scripts

      Public
      Repository for Bichrom-GAT scripts
      Python
      •1•0•0•0•Updated May 25, 2024May 25, 2024

    • chromdisco

      Public
      A fork of tfmodisco for chromatin interpretation
      Python
      •
      MIT License
      •26•0•0•0•Updated Apr 15, 2024Apr 15, 2024

    • Bichrom-Regression

      Public
      Transcription factor binding strength prediction by deep neural network
      Python
      •
      MIT License
      •3•1•0•0•Updated Feb 2, 2024Feb 2, 2024

    • iFox-mES

      Public
      UCSC trackhub links for Mahony lab iFox ChIP-exo analysis
      Python
      •
      MIT License
      •2•1•0•0•Updated Sep 29, 2023Sep 29, 2023

    • Bichrom

      Public
      Interpretable bimodal network for transcription factors binding site prediction
      Python
      •
      MIT License
      •3•10•0•0•Updated Jun 29, 2023Jun 29, 2023

    • mazzoni-zbtb-trackhub

      Public
      Trackhub for Mazzoni lab mES ZBTB ChIP-seq tracks
      HTML
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2023Feb 10, 2023

    • seqview-web-docker-public

      Public
      Wrapper for existing genome browsers to search for files based on their metadata.
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 27, 2023Jan 27, 2023

    • shap-hypothetical

      Public
      A game theoretic approach to explain the output of any machine learning model.
      Jupyter Notebook
      •
      MIT License
      •3.5k•0•0•0•Updated Jan 25, 2023Jan 25, 2023

    • WaveNet

      Public
      Yet another WaveNet implementation in PyTorch.
      Python
      •31•0•0•0•Updated Jan 4, 2023Jan 4, 2023

    • multispecies-domain-adaptation

      Public
      Python
      •0•0•0•0•Updated Oct 6, 2022Oct 6, 2022

    • cross-species-domain-adaptation

      Public
      Codebase for the domain adaptation (cross-species TF binding prediction) project.
      transcription-factorsdeep-learninggenomicscomparative-genomicsdomain-adaptation
      Jupyter Notebook
      •
      MIT License
      •6•12•1•0•Updated Aug 29, 2022Aug 29, 2022

    • sequnwinder

      Public
      SeqUnwinder: a platform for deconvolving motifs associated with genomic labels
      Java
      •
      MIT License
      •0•7•2•0•Updated Aug 29, 2022Aug 29, 2022

    • multigps

      Public
      MultiGPS: software for analyzing collections of multi-condition ChIP-seq datasets
      Java
      •
      MIT License
      •2•3•2•0•Updated Aug 29, 2022Aug 29, 2022

    • multimds

      Public
      Python
      •
      MIT License
      •0•1•1•0•Updated Jun 29, 2022Jun 29, 2022

    • pegr-docker

      Public
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Mar 30, 2022Mar 30, 2022

    • stamp

      Public
      STAMP
      C++
      •3•4•1•0•Updated Jan 21, 2022Jan 21, 2022

    • cegr-galaxy

      Public
      CEGR proprietary Galaxy components: pre-processing pipeline, ChIP-exo statistics tools, etc.
      Python
      •2•3•1•0•Updated Dec 1, 2021Dec 1, 2021

    • domain_adaptive_nn

      Public
      Cross-species TF binding prediction
      Jupyter Notebook
      •1•0•0•0•Updated Oct 17, 2021Oct 17, 2021

    • igv-webapp-embeddable

      Public
      IGV Web App
      JavaScript
      •
      MIT License
      •50•0•1•0•Updated Aug 10, 2021Aug 10, 2021

    • yep-trackhubs

      Public
      UCSC genome browser trackhubs for YEP project
      HTML
      •0•0•0•0•Updated Dec 23, 2020Dec 23, 2020

    • chexalign

      Public
      ChExAlign: alignment and quantification of ChIP-exo crosslinking patterns
      Java
      •
      MIT License
      •0•2•1•0•Updated Aug 6, 2020Aug 6, 2020