Lareau, CalebAryee, Martin2018-04-192017Lareau, Caleb A., and Martin J Aryee. 2017. “diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.” Bioinformatics 34 (4): 672-674. doi:10.1093/bioinformatics/btx623. http://dx.doi.org/10.1093/bioinformatics/btx623.http://nrs.harvard.edu/urn-3:HUL.InstRepos:35982229Abstract Summary The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state. Availability and implementation Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html Contact aryee.martin@mgh.harvard.edu Supplementary information Supplementary data are available at Bioinformatics online.en-USGenome AnalysisJournal Article2018-04-1910.1093/bioinformatics/btx623