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

Lareau, C.; Aryee, M.

doi:10.1101/087338

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bioRxiv · 10.1101/087338

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

Lareau, C.·Aryee, M.

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Abstract

The three-dimensional architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in loop structure are associated with differences in gene expression and cell state. Here, we introduce diffloop, an R/Bioconductor package for identifying differential DNA looping between samples. The package additionally provides a suite of functions for the quality control, statistical testing, annotation and visualization of DNA loops. We demonstrate this functionality by detecting differences in DNA loops between ENCODE ChIA-PET datasets and relate looping to differences in epigenetic state and gene expression.

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Lareau, C., Aryee, M.. 2016-12-24. diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. https://doi.org/10.1101/087338

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