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diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
<span title="2017-09-29">2017</span>
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The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Lareau, 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. Abstract Summary: The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a
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... t, 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
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