Chromatin looping is an important feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in close physical proximity of regulated target genes. Here, we provide a tool 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 can be used to associate enhancers or transcription factor binding sites (e.g. ChIP-seq peaks) to regulated target genes.
|Bioconductor views||Annotation ChIPSeq ChIPchip Classification Coverage DNA3DStructure DataImport Epigenetics FunctionalGenomics HiC Regression|
|Package repository||View on GitHub|
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