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.