An R package for systematically assessing the difference in gene-gene regulatory relationships under different conditions. DGCA contains functions to filter, process, save, visualize, and interpret differential correlations of identifier-pairs across the entire identifier space, or with respect to a particular set of identifiers (e.g., one). It also contains several functions to perform differential correlation analysis on clusters (i.e., modules) or genes. Finally, it proposes functions to generate empirical p-values for the hypothesis tests and adjust them for multiple comparisons. This user-friendly, effective, and comprehensive software tool will facilitate the application of differential correlation analysis in many biological studies and thus will help identification of novel signalling pathways, biomarkers, and targets in complex biological systems and diseases.