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bioRxiv · 10.1101/526269

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

Cairns, J.·Orchard, W. R.·Malysheva, V.·Spivakov, M.
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Abstract

SummaryCapture 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.

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Cairns, J., Orchard, W. R., Malysheva, V., Spivakov, M.. 2019-01-22. Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data. https://doi.org/10.1101/526269

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