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

作者：Lareau Caleb A; Aryee Martin J

来源：Bioinformatics, 2018, 34(4): 672-674.

DOI：10.1093/bioinformatics/btx623

<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Summary</jats:title>
<jats:p>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.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Availability and implementation</jats:title>
<jats:p>Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Supplementary information</jats:title>
<jats:p>Supplementary data are available at Bioinformatics online.</jats:p>
</jats:sec>

• 出版日期2018-2-15