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 |