gage: Generally Applicable Gene-set Enrichment for Pathway Analysis
Version 2.26.0

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

Browse man pages Browse package API and functions Browse package files

AuthorWeijun Luo
Bioconductor views DifferentialExpression GO GeneExpression GeneSetEnrichment Genetics Microarray MultipleComparison OneChannel Pathways RNASeq Sequencing SystemsBiology TwoChannel
Date of publicationNone
MaintainerWeijun Luo <luo_weijun@yahoo.com>
LicenseGPL (>=2.0)
Version2.26.0
URL http://www.biomedcentral.com/1471-2105/10/161
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gage")

Man pages

eg2sym: Conversion between Entrez Gene IDs and official gene symbols...
egSymb: Mapping between Entrez Gene IDs and official symbols
esset.grp: The non-redundant signcant gene set list
essGene: Essential member genes in a gene set
gage: GAGE (Generally Applicable Gene-set Enrichment) analysis
gageComp: Compare multiple GAGE analyses results
gage-internal: Internal functions
gagePipe: GAGE analysis pipeline
geneData: View the expression data for selected genes
go.gsets: Generate up-to-date GO (Gene Ontology) gene sets
gse16873: GSE16873: a breast cancer microarray dataset
gs.tTest: Gene set differential expression test
heter.gage: GAGE analysis for heterogeneous data
kegg.gs: Common gene set data collections
kegg.gsets: Generate up-to-date KEGG pathway gene sets
readExpData: Read in expression data
readList: Read in gene set data as a named list
sigGeneSet: Significant gene set from GAGE analysis

Functions

bods Man page
carta.gs Man page
colorpanel Man page Source code
deComp Man page Source code
eg2sym Man page Source code
egSymb Man page
essGene Man page Source code
esset.grp Man page Source code
gage Man page Source code
gageComp Man page Source code
gagePipe Man page Source code
gagePrep Man page Source code
gageSum Man page Source code
geneData Man page Source code
go.gs Man page
go.gsets Man page Source code
greenred Man page Source code
gs.KSTest Man page Source code
gs.heatmap Man page Source code
gs.tTest Man page Source code
gs.zTest Man page Source code
gse16873 Man page
heatmap2 Man page Source code
heter.gage Man page Source code
invalid Man page Source code
kegg.gs Man page
kegg.gs.dise Man page
kegg.gsets Man page Source code
kegg.species.code Man page Source code
khier Man page
korg Man page
odd Man page Source code
pairData Man page Source code
readExpData Man page Source code
readList Man page Source code
rownorm Man page Source code
sigGeneSet Man page Source code
sym2eg Man page Source code
vennCounts Man page Source code
vennDiagram2 Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/colorpanel.R
R/deComp.R
R/eg2sym.R
R/essGene.R
R/esset.grp.R
R/gage-internal.R
R/gage.R
R/gageComp.R
R/gagePipe.R
R/gagePrep.R
R/gageSum.R
R/geneData.R
R/go.gsets.R
R/greenred.R
R/gs.KSTest.R
R/gs.heatmap.R
R/gs.tTest.R
R/gs.zTest.R
R/heatmap2.R
R/heter.gage.R
R/invalid.R
R/kegg.gsets.R
R/kegg.species.code.R
R/odd.R
R/pairData.R
R/readExpData.R
R/readList.R
R/rownorm.R
R/sigGeneSet.R
R/sym2eg.R
R/vennCounts.R
R/vennDiagram2.R
build
build/vignette.rds
data
data/bods.rda
data/carta.gs.rda
data/datalist
data/egSymb.rda
data/go.gs.rda
data/gse16873.rda
data/kegg.gs.dise.rda
data/kegg.gs.rda
data/khier.rda
data/korg.rda
inst
inst/CITATION
inst/doc
inst/doc/RNA-seqWorkflow.R
inst/doc/RNA-seqWorkflow.Rnw
inst/doc/RNA-seqWorkflow.pdf
inst/doc/dataPrep.R
inst/doc/dataPrep.Rnw
inst/doc/dataPrep.pdf
inst/doc/gage.R
inst/doc/gage.Rnw
inst/doc/gage.pdf
inst/extdata
inst/extdata/c2.demo.gmt
inst/extdata/gse16873.demo
man
man/eg2sym.Rd
man/egSymb.Rd
man/essGene.Rd
man/esset.grp.Rd
man/gage-internal.Rd
man/gage.Rd
man/gageComp.Rd
man/gagePipe.Rd
man/geneData.Rd
man/go.gsets.Rd
man/gs.tTest.Rd
man/gse16873.Rd
man/heter.gage.Rd
man/kegg.gs.Rd
man/kegg.gsets.Rd
man/readExpData.Rd
man/readList.Rd
man/sigGeneSet.Rd
vignettes
vignettes/RNA-seqWorkflow.Rnw
vignettes/dataPrep.Rnw
vignettes/gage.Rnw
vignettes/gage.bib
gage documentation built on May 20, 2017, 10:32 p.m.