gage: Generally Applicable Gene-set Enrichment for Pathway Analysis

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.

AuthorWeijun Luo
Date of publicationNone
MaintainerWeijun Luo <luo_weijun@yahoo.com>
LicenseGPL (>=2.0)
Version2.24.0
http://www.biomedcentral.com/1471-2105/10/161

View on Bioconductor

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.