To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EGSEA")

In most cases, you don't need to download the package archive at all.

EGSEA

   

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see EGSEA.

Ensemble of Gene Set Enrichment Analyses

Bioconductor version: 3.3

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.

Author: Monther Alhamdoosh, Milica Ng and Matthew Ritchie

Maintainer: Monther Alhamdoosh <m.hamdoosh at gmail.com>

Citation (from within R, enter citation("EGSEA")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EGSEA")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EGSEA")

 

PDF R Script EGSEA vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, Genetics, GraphAndNetwork, KEGG, Metabolomics, Microarray, MultipleComparison, OneChannel, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, TwoChannel
Version 1.0.3
In Bioconductor since BioC 3.3 (R-3.3) (< 6 months)
License GPL-2
Depends R (>= 3.3), Biobase, gage(>= 2.14.4), AnnotationDbi, topGO(>= 2.16.0), pathview(>= 1.4.2)
Imports PADOG(>= 1.6.0), GSVA(>= 1.12.0), globaltest(>= 5.18.0), limma(>= 3.20.9), edgeR(>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe(>= 3.4.0), stringi (>= 0.5.0), parallel, stats, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, EGSEAdata
LinkingTo
Suggests BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me EGSEAdata
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source EGSEA_1.0.3.tar.gz
Windows Binary EGSEA_1.0.3.zip
Mac OS X 10.9 (Mavericks) EGSEA_1.0.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/EGSEA/tree/release-3.3
Package Short Url http://bioconductor.org/packages/EGSEA/
Package Downloads Report Download Stats

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