diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Author(s)
Lun, AT; Smyth, GK;
Details
Publication Year 2015,Volume 16,Issue #1,Page 258
Journal Title
BMC Bioinformatics
Publication Type
Journal Article
Abstract
BACKGROUND: Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions. However, an alternative strategy involves identifying significant changes in the interaction intensity (i.e., differential interactions) between two or more biological conditions. This is more statistically rigorous and may provide more biologically relevant results. RESULTS: Here, we present the diffHic software package for the detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. The use of diffHic is demonstrated with real Hi-C data sets. Performance against existing methods is also evaluated with simulated data. CONCLUSIONS: On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. These results suggest that diffHic is a viable approach for differential analyses of Hi-C data.
Publisher
BioMed Central
Research Division(s)
Bioinformatics
PubMed ID
26283514
Open Access at Publisher's Site
http://www.biomedcentral.com/1471-2105/16/258
NHMRC Grants
NHMRC/1054618
Terms of Use/Rights Notice
Refer to copyright notice on published article.


Creation Date: 2015-08-21 12:29:32
Last Modified: 2015-09-01 03:50:42
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