HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular .tsv files, Cooler .cool or .mcool files, Juicer .hic files or HiC-Pro .matrix and .bed files.