gage

Generally Applicable Gene-set Enrichment for Pathway Analysis

Bioconductor version: Release (2.7)

GAGE is a published method for gene set or pathway analysis. In gage package, we provide a series of functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analysis on different comparisons or samples, the comparison of parallel analysis results, and even the combined analysis of heterogeneous data from different sources/studies. In addition, we also 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

Maintainer: Weijun Luo

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("gage")    

Documentation

PDF

R Script

Generally Applicable Gene-set/Pathway Analysis

Reference Manual

Details

biocViews	Pathways, GO, DifferentialExpression, Microarray, OneChannel, TwoChannel, RNAseq, DataRepresentation, Genetics, Bioinformatics, MultipleComparisons
Depends	graph, multtest
Imports
Suggests	gageData, GO.db, GSEABase, KEGG.db, org.Hs.eg.db
System Requirements
License	GPL (>=2.0)
URL
Depends On Me
Imports Me
Suggests Me
Version	2.0.0

Package Downloads

Package Source	gage_2.0.0.tar.gz
Windows Binary	gage_2.0.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	gage_2.0.0.tgz
Package Downloads Report	Download Stats