rGREAT: Client for GREAT Analysis
Version 1.8.0

This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.

Browse man pages Browse package API and functions Browse package files

AuthorZuguang Gu
Bioconductor views Coverage GO GeneSetEnrichment GenomeAnnotation Pathways Sequencing Software WholeGenome
Date of publication2017-2-8 00:00:00
MaintainerZuguang Gu <z.gu@dkfz.de>
LicenseGPL (>= 2)
Version1.8.0
URL https://github.com/jokergoo/rGREAT
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rGREAT")

Man pages

availableCategories-GreatJob-method: Available ontology categories
availableOntologies-GreatJob-method: All available ontology names
getEnrichmentTables-GreatJob-method: Get enrichment tables from GREAT web server
GreatJob-class: Class to store and retrieve GREAT results
plotRegionGeneAssociationGraphs-GreatJob-method: Plot region-gene association figures
submitGreatJob: Send requests to GREAT web server

Functions

GREAT.read.json Source code
GreatJob-class Man page
availableCategories Man page
availableCategories,GreatJob-method Man page
availableOntologies Man page
availableOntologies,GreatJob-method Man page
check_asso_file Source code
download Source code
getEnrichmentTables Man page
getEnrichmentTables,GreatJob-method Man page
parseRegionGeneAssociationFile Source code
plotRegionGeneAssociationGraphs Man page
plotRegionGeneAssociationGraphs,GreatJob-method Man page
sleep Source code
sort_chr Source code
submitGreatJob Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/00_S4_generic_methods.R
R/global.R
R/great.R
build
build/vignette.rds
inst
inst/doc
inst/doc/rGREAT.R
inst/doc/rGREAT.Rmd
inst/doc/rGREAT.html
inst/extdata
inst/extdata/job.rds
inst/tests
man
man/GreatJob-class.rd
man/availableCategories-GreatJob-method.rd
man/availableOntologies-GreatJob-method.rd
man/getEnrichmentTables-GreatJob-method.rd
man/plotRegionGeneAssociationGraphs-GreatJob-method.rd
man/submitGreatJob.rd
test
tests
tests/test-all.R
tests/testthat
tests/testthat/test_available.R
tests/testthat/test_great.R
vignettes
vignettes/custom.css
vignettes/rGREAT.Rmd
rGREAT documentation built on May 20, 2017, 10:07 p.m.