Man pages for jokergoo/rGREAT
GREAT Analysis - Functional Enrichment on Genomic Regions
| 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-dispatch | Method dispatch page for getEnrichmentTable |
| getEnrichmentTable-GreatJob-method | Get a single enrichment table from GREAT web server |
| getEnrichmentTable-GreatObject-method | Get enrichment table |
| getEnrichmentTables-dispatch | Method dispatch page for getEnrichmentTables |
| getEnrichmentTables-GreatJob-method | Get enrichment tables from GREAT web server |
| getEnrichmentTables-GreatObject-method | Get enrichment table |
| 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 |
| getGREATDefaultTSS | Get built-in TSS from GREAT |
| getKEGGGenome | Get the corresponding assembly id for a kegg organism |
| getKEGGPathways | Get KEGG pathway gene sets |
| getRefSeqGenesFromUCSC | Get RefSeq genes from UCSC |
| getRegionGeneAssociations-dispatch | 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 |
| 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 |
| great_opt | Global parameters for rGREAT |
| plotRegionGeneAssociationGraphs-GreatJob-method | Plot region-gene associations |
| plotRegionGeneAssociations-dispatch | Method dispatch page for plotRegionGeneAssociations |
| plotRegionGeneAssociations-GreatJob-method | Plot region-gene associations |
| plotRegionGeneAssociations-GreatObject-method | Plot region-gene associations |
| plotVolcano-dispatch | 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-dispatch | 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 |
