Our team has developed several packages to complement the functionality of clusterProfiler. ChIPseeker10 bridges the genomic region with functional enrichment by annotating the genomic region to associated genes. GOSemSim11 provides more than five methods for measuring semantic similarity. It allows removal of redundant terms using semantic similarities among GO terms and allows enrichment results to be visualized in semantic space so that similar terms cluster together. The DOSE24 package supports functional enrichment from the disease perspective, including disease ontology, the network of cancer genes, and disease gene network. The ReactomePA25 and meshes26 packages support functional analysis using Reactome Pathways and Medical Subject Headings, respectively. DOSE, ReactomePA, and meshes are developed within the framework of clusterProfiler, and the enrichment analysis functions provided in these packages can be used in compareCluster for the comparison of functional profiles under various conditions and at different time points. The enrichplot package provides several visualization methods to generate publication-quality figures to help users interpret the results (Figures 1, 2, 3, and 4; supplemental information). This package suite provides a comprehensive set of tools for mining biological knowledge to elucidate and interpret molecular mechanisms (Figure 6).
