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Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data

By Jonathan Cairns, William R. Orchard, Valeriya Malysheva, Mikhail spivakov

Posted 22 Jan 2019
bioRxiv DOI: 10.1101/526269 (published DOI: 10.1093/bioinformatics/btz450)

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. Chicdiff 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.

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