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 is one of the most popular Bioconductor packages. It has been incorporated in more than 30 CRAN and Bioconductor packages (Table S1), several pipelines (e.g., The Cancer Genome Atlas [TCGA] Workflow12 and ViralLink13), and online platforms (e.g., NASQAR14 and ABioTrans15).Table 1Major clusterProfiler functionsFunctionDescriptionenrichGOORA using GOenrichKEGGORA using KEGG pathwayenrichMKEGGORA using KEGG moduleenrichWPORA using WikiPathwaysenrichergeneral interface for ORAgseGOGSEA using GOgseKEGGGSEA using KEGG pathwaygseMKEGGGSEA using KEGG modulegseWPGSEA using WikiPathwaysGSEAgeneral interface for GSEAcompareClustercompare functional profiles for genes obtained from different conditionsmerge_resultmerge enrichment results for comparisonread.gmtparse gene set file in GMT formatread.gmt.wpparse WikiPathways GMT filedownload_KEGGdownload the latest version of the KEGG pathway/moduleget_wp_organismlist supported organisms of WikiPathwaysbitrbiological ID translator using OrgDbbitr_keggbiological ID translator using the KEGG databasesetReadableconvert IDs in enrichment result to human-readable gene symbols using OrgDbgo2ontconvert GO ID to corresponding ontology (BP, CC, MF)go2termconvert GO ID to a descriptive termko2nameconvert KO ID to a descriptive namebuildGOmapinfer GO indirect annotation from direct annotationbrowseKEGGopen specific KEGG pathway in a web browser with genes highlighteddropGOdrop GO terms of
