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

• DOI: 10.1093/bioinformatics/btz450
• Publication Date: 2019-06-06T03:19:10Z
• Authors: Jonathan Cairns; William R Orchard; Valeriya Malysheva; Mikhail Spivakov
• Keywords: R package; Bespoke; Normalization

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 robust detection differential in data. Chicdiff enhances state-of-the-art testing count data with bespoke normalization and multiple procedures that account specific statistical properties Hi-C. validate published Promoter human Monocytes CD4+ T cells, identifying multitudes cell type-specific interactions, confirming the overall positive association between promoter expression.Chicdiff implemented publicly available https://github.com/RegulatoryGenomicsGroup/chicdiff.Supplementary are Bioinformatics online.