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| GeneAnswers-package | Integrated Interpretation of Genes |
| 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 |
| class:GeneAnswers | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| DmIALite | Fly gene interaction matrix |
| DO | Several data objects related with DO (Disease Ontology) and its mapping to genes |
| DO.graph.closure.gene | Several data objects related with DO (Disease Ontology) and its mapping to genes |
| DO.graph.gene | Several data objects related with DO (Disease Ontology) and its mapping to genes |
| DO.terms | Several data objects related with DO (Disease Ontology) and its mapping to genes |
| DO2gene.map | Several data objects related with DO (Disease Ontology) and its mapping to genes |
| DOLite | Disease Ontology Annotation List |
| DOLiteTerm | Disease Ontology Annotation Vector |
| drawTable | Concept-Gene Networking Plotting |
| entrez2caBIO | map Entrez gene IDs to caBIO gene IDs |
| gene2DO.map | Several data objects related with DO (Disease Ontology) and its mapping to genes |
| geneAnnotationHeatmap | Make a concept-gene cross tabulation |
| GeneAnswers | Integrated Interpretation of Genes |
| GeneAnswers-class | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| 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 |
| getAnnLib | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getAnnLib-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getcaBIOPATHList | Retrieve caBIO path categories containing given genes |
| getcaBIOPATHTerms | Get Pathway names of given REACTOME PATH_DB IDs |
| getCategoryList | Retrieve categories containing given genes |
| getCategoryTerms | Mapping Category IDs to Terms |
| getCategoryType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getCategoryType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getConceptTable | Generate top concepts-genes table |
| getConnectedGraph | build and display a network for given IDs |
| getDOLiteTerms | Get DOLite Terms of Given DOLite IDs |
| getEnrichmentInfo | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getEnrichmentInfo-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getGeneExprProfile | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getGeneExprProfile-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getGeneInput | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getGeneInput-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getGenesInCategory | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getGenesInCategory-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| 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 |
| getPValueT | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getPValueT-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| 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 |
| getTestType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getTestType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| getTotalGeneNumber | Obtain the total number of genes in the given annotation library |
| groupReport | Generate a multigroup Concepts-genes analysis report |
| HsIALite | Human gene interaction matrix |
| humanExpr | Example human expression data |
| humanGeneInput | Example human gene data |
| MmIALite | Mouse gene interaction matrix |
| mouseExpr | Example mouse expression data |
| mouseGeneInput | Example mouse gene data |
| RnIALite | Rat gene interaction matrix |
| sampleGroupsData | Example human expression data |
| searchEntrez | Search specified information from Entrez site |
| setAnnLib | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setAnnLib-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setCategoryType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setCategoryType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setEnrichmentInfo | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setEnrichmentInfo-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setGeneExprProfile | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setGeneExprProfile-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setGeneInput | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setGeneInput-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setGenesInCategory | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setGenesInCategory-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setPValueT | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setPValueT-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setTestType | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| setTestType-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| show | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| show-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| summary | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| summary-method | Class GeneAnswers: contain and describe the relationship between given gene data and specified category |
| topcaBIO.PATH | Present top CABIO.PATH enrichment test information |
| topcaBIO.PATHGenes | Present top CABIO.PATH enrichment test information with genes |
| 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 |