source("http://bioconductor.org/biocLite.R")
biocLite("PADOG")

PADOG

Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

Bioconductor version: 2.13

This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.

Author: Adi Laurentiu Tarca <atarca at med.wayne.edu>

Maintainer: Adi Laurentiu Tarca <atarca at med.wayne.edu>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("PADOG")

Documentation

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

browseVignettes("PADOG")

 

PDF	R Script	PADOG
PDF		Reference Manual

Details

biocViews	Bioinformatics, Microarray, OneChannel, Software, TwoChannel
Version	1.4.0
In Bioconductor since	BioC 2.11 (R-2.15)
License	GPL (>= 2)
Depends	R (>= 2.14.0), KEGGdzPathwaysGEO, graphics, limma, AnnotationDbi, Biobase, methods, nlme, GSA, KEGG.db
Imports	graphics, limma, hgu133plus2.db, hgu133a.db, KEGG.db, AnnotationDbi, Biobase, methods, nlme
Suggests	parallel
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source	PADOG_1.4.0.tar.gz
Windows Binary	PADOG_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	PADOG_1.4.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats