IDR2D identifies reproducible genomic interactions

Chromatin interaction data from protocols such as ChIA-PET and HiChIP provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce a generalization of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments.