ALLEXTID                Get all background External ID.
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 Information content and DO term to
                        entrez gene IDs mapping
EXTID2NAME              EXTID2NAME
EXTID2TERMID            Mapping External ID to Ontology Term ID
TERM2NAME               Mapping Ontology Term ID to Name Symbol or
                        Description
TERMID2EXTID            Mapping Ontology Term ID to External ID
barplot.enrichResult    barplot
cnetplot                cnetplot method
cnetplot.internal       plot gene net by categories
computeIC               compute information content
doSim                   doSim
enrich.internal         enrich.internal
enrichDO                DO Enrichment Analysis of a gene set.
enrichResult-class      Class "enrichResult" This class represents the
                        result of enrichment analysis.
gene2DO                 convert Gene ID to DO Terms
geneSim                 geneSim
getALLEG                getALLEG
getGeneSet              preparing geneSets for gene set enrichment
                        analysis
gseAnalyzer             Gene Set Enrichment Analysis
gsea                    gsea
gseaResult-class        Class "gseaResult" This class represents the
                        result of GSEA analysis
gseaplot                visualize analyzing result of GSEA
list2graph              convert gene IDs to igraph object
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
