GreatJob                Constructor method for GreatJob class
GreatJob-class          Class to store and retrieve GREAT results
GreatObject             Constructor method for GreatObject class
GreatObject-class       Class for local GREAT analysis
availableCategories,GreatJob-method
                        Available ontology categories of the GREAT job
availableOntologies,GreatJob-method
                        All available ontology names of the GREAT job
extendTSS               Extend TSS
extendTSSFromDataFrame
                        Extend TSS
extendTSSFromOrgDb      Extend TSS
extendTSSFromTxDb       Extend TSS
getEnrichmentTable      Method dispatch page for getEnrichmentTable
getEnrichmentTable,GreatJob-method
                        Get a single enrichment table from GREAT web
                        server
getEnrichmentTable,GreatObject-method
                        Get enrichment table
getEnrichmentTables     Method dispatch page for getEnrichmentTables
getEnrichmentTables,GreatJob-method
                        Get enrichment tables from GREAT web server
getEnrichmentTables,GreatObject-method
                        Get enrichment table
getGREATDefaultTSS      Get built-in TSS from GREAT
getGapFromUCSC          Get gap regions from UCSC
getGeneSetsFromBioMart
                        Get GO gene sets from BioMart
getGeneSetsFromOrgDb    Get GO gene sets from OrgDb object
getGenesFromGencode     Get Gencode genes
getGenomeDataFromNCBI   Get genome data from NCBI
getKEGGGenome           Get the corresponding assembly id for a kegg
                        organism
getKEGGPathways         Get KEGG pathway gene sets
getRefSeqGenesFromUCSC
                        Get RefSeq genes from UCSC
getRegionGeneAssociations
                        Method dispatch page for
                        getRegionGeneAssociations
getRegionGeneAssociations,GreatJob-method
                        Get region-gene associations
getRegionGeneAssociations,GreatObject-method
                        Get region-gene associations
getTSS                  Get the internally used TSS
great                   Perform GREAT analysis
great_opt               Global parameters for rGREAT
plotRegionGeneAssociationGraphs,GreatJob-method
                        Plot region-gene associations
plotRegionGeneAssociations
                        Method dispatch page for
                        plotRegionGeneAssociations
plotRegionGeneAssociations,GreatJob-method
                        Plot region-gene associations
plotRegionGeneAssociations,GreatObject-method
                        Plot region-gene associations
plotVolcano             Method dispatch page for plotVolcano
plotVolcano,GreatJob-method
                        Make volcano plot
plotVolcano,GreatObject-method
                        Make volcano plot
randomRegions           Generate random regions
randomRegionsFromBioMartGenome
                        Generate random regions from a BioMart genome
read_gmt                Read gmt gene sets file
reduce_by_start_and_end
                        Reduce by start and end
shinyReport             Method dispatch page for shinyReport
shinyReport,GreatJob-method
                        Shiny app on the GreatJob object
shinyReport,GreatObject-method
                        Shiny app on the GreatObject object
submitGreatJob          Perform online GREAT analysis
