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

Bioinformatics. 2018 Feb 15;34(4):672-674. doi: 10.1093/bioinformatics/btx623.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromatin / metabolism
  • Chromatin / ultrastructure*
  • Chromatin Immunoprecipitation / methods
  • Epigenomics
  • Humans
  • K562 Cells
  • MCF-7 Cells
  • Molecular Sequence Annotation / methods*
  • Neoplasms / genetics
  • Sequence Analysis, DNA / methods*
  • Software*


  • Chromatin