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
barplot.enrichResult    barplot
clusterSim              clusterSim
cnetplot                cnetplot method
cnetplot_internal       cnetplot_internal
computeIC               compute information content
doSim                   doSim
dotplot                 dotplot method
enrichDO                DO Enrichment Analysis
enrichMap               enrichMap
enrichNCG               enrichNCG
enrichResult-class      Class "enrichResult" This class represents the
                        result of enrichment analysis.
enricher_internal       enrich.internal
fortify.enrichResult    fortify
fortify.gseaResult      fortify.gseaResult
gene2DO                 convert Gene ID to DO Terms
geneSim                 geneSim
gseDO                   DO Gene Set Enrichment Analysis
gseNCG                  NCG Gene Set Enrichment Analysis
gseaResult-class        Class "gseaResult" This class represents the
                        result of GSEA analysis
gseaplot                visualize analyzing result of GSEA
gsfilter                gsfilter
list2graph              convert gene IDs to igraph object
load_OrgDb              load_OrgDb
mclusterSim             mclusterSim
netplot                 netplot
plot                    plot method
rebuildAnnoData         rebuiding annotation data
scaleNodeColor          scaleNodeColor
setReadable             setReadable
setting.graph.attributes
                        setting.graph.attributes
show                    show method
simplot                 simplot
summary                 summary method
theme_dose              theme_dose
upsetplot               upsetplot method
