To install this package, start R and enter:

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

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

PADOG

 

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

Bioconductor version: Release (3.1)

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>; Zhonghui Xu <zhonghui.xu at gmail.com>

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

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

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 Microarray, OneChannel, Software, TwoChannel
Version 1.10.0
In Bioconductor since BioC 2.11 (R-2.15) (3 years)
License GPL (>= 2)
Depends R (>= 3.0.0), KEGGdzPathwaysGEO, methods, Biobase
Imports limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGG.db, nlme
LinkingTo
Suggests doParallel, parallel
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source PADOG_1.10.0.tar.gz
Windows Binary PADOG_1.10.0.zip
Mac OS X 10.6 (Snow Leopard) PADOG_1.10.0.tgz
Mac OS X 10.9 (Mavericks) PADOG_1.10.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/PADOG/tree/release-3.1
Package Short Url http://bioconductor.org/packages/PADOG/
Package Downloads Report Download Stats

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