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Media type:
E-Article
Title:
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
Contributor:
Lareau, Caleb A;
Aryee, Martin J
imprint:
Oxford University Press (OUP), 2018
Published in:Bioinformatics
Language:
English
DOI:
10.1093/bioinformatics/btx623
ISSN:
1367-4803;
1367-4811
Origination:
Footnote:
Description:
<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>