Compares profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). DChIPRep tests for differential enrichment at each nucleotide position of a metagene/metafeature profile and determines positions with significant differences in enrichment between experimental groups. DChIPRep provides two plotting functions to represent and inspect the final results of the analysis. The yeast case study demonstrates DChIPRep’s favourable performance when compared to a pipeline inspired by the csaw-package for differential binding analysis.