PADOG

DOI: 10.18129/B9.bioc.PADOG    

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

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PADOG")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.30.0
In Bioconductor since	BioC 2.11 (R-2.15) (8 years)
License	GPL (>= 2)
Depends	R (>= 3.0.0), KEGGdzPathwaysGEO, methods, Biobase
Imports	limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme
LinkingTo
Suggests	doParallel, parallel
SystemRequirements
Enhances
URL
Depends On Me	BLMA
Imports Me	EGSEA
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	PADOG_1.30.0.tar.gz
Windows Binary	PADOG_1.30.0.zip
macOS 10.13 (High Sierra)	PADOG_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PADOG
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PADOG
Package Short Url	https://bioconductor.org/packages/PADOG/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive