PADOG

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("PADOG")

Documentation

PDF R Script PADOG
PDF   Reference Manual

Details

biocViews Microarray, OneChannel, Software, TwoChannel
Version 1.7.0
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 Downloads

Package Source PADOG_1.7.0.tar.gz
Windows Binary PADOG_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) PADOG_1.7.0.tgz
Mac OS X 10.9 (Mavericks)
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