DO                      Several data objects related with DO (Disease
                        Ontology) and its mapping to genes
DOLite                  Disease Ontology Annotation List
DOLiteTerm              Disease Ontology Annotation Vector
DmIALite                Fly gene interaction matrix
GeneAnswers-class       Class GeneAnswers: contain and describe the
                        relationship between given gene data and
                        specified category
GeneAnswers-package     Integrated Interpretation of Genes
HsIALite                Human gene interaction matrix
MmIALite                Mouse gene interaction matrix
RnIALite                Rat gene interaction matrix
buildNet                build and display a network for given IDs and
                        interaction Matrix
caBIO2entrez            map caBIO gene IDs to Entrez gene IDs
categoryNet             Plot Category Links
chartPlots              Pie Chart and Bar Plots
drawTable               Concept-Gene Networking Plotting
entrez2caBIO            map Entrez gene IDs to caBIO gene IDs
geneAnnotationHeatmap   Make a concept-gene cross tabulation
geneAnswersBuilder      Build an object of a GeneAnswers class
geneAnswersChartPlots   Make pie chart and bar plot
geneAnswersConceptNet   Concept-Gene Networking Plotting
geneAnswersConceptRelation
                        Display a network related to given concepts for
                        a GeneAnswers instance
geneAnswersConcepts     Concept-Gene Networking Plotting
geneAnswersHeatmap      Generate Concept-Gene Tabulates
geneAnswersHomoMapping
                        Mapping homogenes for a GeneAnswers instance
geneAnswersReadable     Make GeneAnswers Instance readable
geneAnswersSort         Sort enrichmentInfo of a GeneAnswers instance
geneConceptNet          Generate Concept-gene network
getCategoryList         Retrieve categories containing given genes
getCategoryTerms        Mapping Category IDs to Terms
getConceptTable         Generate top concepts-genes table
getConnectedGraph       build and display a network for given IDs
getDOLiteTerms          Get DOLite Terms of Given DOLite IDs
getGOList               Get GO list of given genes
getHomoGeneIDs          Get homologous genes of given genes
getListGIF              getListGIF
getMultiLayerGraphIDs   retrieve multilayer interacted nodes for given
                        IDs and interaction Matrix
getNextGOIDs            retrieve parents or children GO IDs for given
                        GO IDs
getPATHList             Retrieve KEGG categories containing given genes
getPATHTerms            Get Pathway names of given KEGG IDs
getREACTOMEPATHList     Retrieve REACTOME path categories containing
                        given genes
getREACTOMEPATHTerms    Get Pathway names of given REACTOME PATH_DB IDs
getSingleLayerGraphIDs
                        retrieve direct interacted nodes for given IDs
                        and interaction Matrix
getSymbols              Convert entrez gene IDs to gene symbols
getTotalGeneNumber      Obtain the total number of genes in the given
                        annotation library
getcaBIOPATHList        Retrieve caBIO path categories containing given
                        genes
getcaBIOPATHTerms       Get Pathway names of given REACTOME PATH_DB IDs
groupReport             Generate a multigroup Concepts-genes analysis
                        report
humanExpr               Example human expression data
humanGeneInput          Example human gene data
mouseExpr               Example mouse expression data
mouseGeneInput          Example mouse gene data
sampleGroupsData        Example human expression data
searchEntrez            Search specified information from Entrez site
topCategory             Present top enrichment test information
topCategoryGenes        Present top enrichment test information with
                        genes
topDOLITE               Present top DOLITE enrichment test information
topDOLITEGenes          Present top DOLITE enrichment test information
                        with genes
topGO                   Present top GO enrichment test information
topGOGenes              Present top GO enrichment test information with
                        genes
topPATH                 Present top KEGG enrichment test information
topPATHGenes            Present top KEGG enrichment test information
                        with genes
topREACTOME.PATH        Present top REACTOME.PATH enrichment test
                        information
topREACTOME.PATHGenes   Present top REACTOME.PATH enrichment test
                        information with genes
topcaBIO.PATH           Present top CABIO.PATH enrichment test
                        information
topcaBIO.PATHGenes      Present top CABIO.PATH enrichment test
                        information with genes
