ibn-salem/chromloop: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.

Getting started

Package details

Bioconductor views Annotation ChIPSeq ChIPchip Classification Coverage DNA3DStructure DataImport Epigenetics FunctionalGenomics HiC Regression
URL https://github.com/ibn-salem/sevenC
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
ibn-salem/chromloop documentation built on May 18, 2019, 1:29 a.m.