DOSE-package Disease Ontology Semantic and Enrichment analysis Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis. DataSet Datasets EXTID2NAME EXTID2NAME GSEA_internal GSEA_internal clusterSim clusterSim compareClusterResult-class Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis. computeIC compute information content doSim doSim enrichDGN Enrichment analysis based on the DisGeNET () enrichDGNv enrichDGN enrichDO DO Enrichment Analysis enrichNCG enrichNCG enrichResult-class Class "enrichResult" This class represents the result of enrichment analysis. enricher_internal enrich.internal gene2DO convert Gene ID to DO Terms geneID geneID generic geneInCategory geneInCategory generic geneSim geneSim gseDGN DisGeNET Gene Set Enrichment Analysis gseDO DO Gene Set Enrichment Analysis gseNCG NCG Gene Set Enrichment Analysis gseaResult-class Class "gseaResult" This class represents the result of GSEA analysis gsfilter gsfilter mclusterSim mclusterSim parse_ratio parse_ratio rebuildAnnoData rebuiding annotation data setReadable setReadable show show method simplot simplot summary summary method theme_dose theme_dose