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

ABSTRACT:

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. Chicdiff enhances a state-of-the-art differential testing approach for count data with bespoke normalization 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.

Availability and implementation

Chicdiff is implemen

SUBMITTER: Cairns J 

PROVIDER: S-EPMC6853696 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature