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.

Author
Weijun Luo
Date of publication
None
Maintainer
Weijun Luo <luo_weijun@yahoo.com>
License
GPL (>=2.0)
Version
2.24.0
URLs

View on Bioconductor

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

Files in this package

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