The clusterProfiler library was first published in 20127 and designed to perform over-representation analysis (ORA)8 using GO and KEGG for several model organisms and to compare functional profiles of various conditions on one level (e.g., different treatment groups). Since then, clusterProfiler has matured substantially and currently supports several ontology and pathway annotations, thousands of species with up-to-date gene annotation, users’ annotation data for novel species, and emerging new annotations. Both ORA and gene set enrichment analysis (GSEA)9 are supported. The comparison utility is extended to support a complex experimental design that allows comparison of functional profiles of various conditions on different levels. The clusterProfiler library has many unique features, including a tidy interface that can manipulate the enrichment result and directly support the visualization of the enrichment result using ggplot2 (Tables 1 and S2). Moreover, we have developed several packages to complement its functionalities, including ChIPseeker to connect functional analysis with genomic ROIs,10 GOSemSim11 to remove redundant GO terms, and enrichplot to visualize the enrichment results. These complementary packages enable clusterProfiler to stand out among other tools. The clusterProfiler library
