# Generally Applicable Gene-set Enrichment for Pathway Analysis

## Documentation for package ‘gage’ version 2.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

bods | Common gene set data collections
carta.gs | Common gene set data collections
eg2sym | Conversion between Entrez Gene IDs and official gene symbols for human genes.
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
gagePipe | GAGE analysis pipeline
gagePrep | GAGE (Generally Applicable Gene-set Enrichment) analysis
gageSum | GAGE (Generally Applicable Gene-set Enrichment) analysis
geneData | View the expression data for selected genes
go.gs | Common gene set data collections
go.gsets | Generate up-to-date GO (Gene Ontology) gene sets
gs.KSTest | Gene set differential expression test
gs.tTest | Gene set differential expression test
gs.zTest | Gene set differential expression test
gse16873 | GSE16873: a breast cancer microarray dataset
heter.gage | GAGE analysis for heterogeneous data
kegg.gs | Common gene set data collections
kegg.gs.dise | Common gene set data collections
kegg.gsets | Generate up-to-date KEGG pathway gene sets
khier | Common gene set data collections
korg | Common gene set data collections
pairData | GAGE analysis for heterogeneous data
readExpData | Read in expression data
readList | Read in gene set data as a named list
sigGeneSet | Significant gene set from GAGE analysis
sym2eg | Conversion between Entrez Gene IDs and official gene symbols for human genes.