Bioconductor-mirror/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.

Getting started

Package details

AuthorWeijun Luo
Bioconductor views DifferentialExpression GO GeneExpression GeneSetEnrichment Genetics Microarray MultipleComparison OneChannel Pathways RNASeq Sequencing SystemsBiology TwoChannel
MaintainerWeijun Luo <[email protected]>
LicenseGPL (>=2.0)
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Bioconductor-mirror/gage documentation built on June 26, 2017, 10:34 p.m.