PT  - JOURNAL ARTICLE
AU  - Jonathan Cairns
AU  - William R. Orchard
AU  - Valeriya Malysheva
AU  - Mikhail Spivakov
TI  - Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data
AID  - 10.1101/526269
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 526269
4099  - http://biorxiv.org/content/early/2019/01/22/526269.1.short
4100  - http://biorxiv.org/content/early/2019/01/22/526269.1.full
AB  - Summary Capture Hi-C is a powerful approach for detecting chromosomal interactions involving, at least on one end, DNA regions of interest, such as gene promoters. We present Chicdiff, an R package for robust detection of differential interactions in Capture Hi-C data. ChiScdiff enhances a state-of-the-art differential testing approach for count data with bespoke normalisation and multiple testing procedures that account for specific statistical properties of Capture Hi-C. We validate Chicdiff on published Promoter Capture Hi-C data in human Monocytes and CD4+ T cells, identifying multitudes of cell type-specific interactions, and confirming the overall positive association between promoter interactions and gene expression. Chicdiff is implemented as an R package that is publicly available at https://github.com/RegulatoryGenomicsGroup/chicdiff.