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
computeIC               compute information content
doSim                   doSim
enrichDGN               Enrichment analysis based on the DisGeNET
                        (<URL: http://www.disgenet.org/>)
enrichDGNv              enrichDGN
enrichDO                DO Enrichment Analysis
enrichNCG               enrichNCG
enrichResult-class      Class "enrichResult" This class represents the
                        result of enrichment analysis.
enricher_internal       enrich.internal
fortify.enrichResult    fortify
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
