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diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

By Caleb A. Lareau, Martin J. Aryee

Posted 24 Dec 2016
bioRxiv DOI: 10.1101/087338 (published DOI: 10.1093/bioinformatics/btx623)

The three-dimensional architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in loop structure are associated with differences in gene expression and cell state. Here, we introduce diffloop, an R/Bioconductor package for identifying differential DNA looping between samples. The package additionally provides a suite of functions for the quality control, statistical testing, annotation and visualization of DNA loops. We demonstrate this functionality by detecting differences in DNA loops between ENCODE ChIA-PET datasets and relate looping to differences in epigenetic state and gene expression.

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