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 |
geneFunSummarize |
Summarize gene functions (annotations) based collective annotation evidences associated with ontology terms |
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 |
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 |
sampleGroupsData |
Example human expression data |
saveGeneFunSummary |
save the summarized gene function as a tab-separated text file |
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 |
simplifyGeneFunSummary |
Simplify the significant ontology terms to a miniSet annotation |
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 |