Fig. 1.

(A) The figure plots the HiCRep score for various pairs of Hi-C experiments, including biological replicates (red), non-replicate experiments of the same cell type (green) and non-replicate experiments of different cell types (blue). Horizontal lines with error bars correspond to the mean and SD of each group. (B) MDS plot based on HiCRep scores from 90 Hi-C experiments carried out on a variety of cell types. (C) Timing comparison of the R and Python implementations of HiCRep for Hi-C matrices with varying bin sizes. Error bars are standard deviation over five runs. Run times for the R implementation beyond 10 kb resolution are not shown, as the program required more memory for these calculations than was available (see Supplementary Fig. S1)