dcHiC

dcHiC is a tool that utilizes a multivariate distance measure to compare multiple contact maps and identify significant changes in their compartmentalization. Evaluated on four collections of bulk and single-cell contact maps, dcHiC was shown to be effective and sensitive in detecting biologically relevant changes, such as associated genes, chromatin states, subcompartments, replication timing, and lamin association. dcHiC is an efficient and powerful tool that enables high-resolution compartment analysis, standalone browser visualization, differential interaction identification, and time-series clustering.