PT  - JOURNAL ARTICLE
AU  - Caleb A. Lareau
AU  - Martin J. Aryee
TI  - diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
AID  - 10.1101/087338
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 087338
4099  - http://biorxiv.org/content/early/2016/12/24/087338.short
4100  - http://biorxiv.org/content/early/2016/12/24/087338.full
AB  - 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.