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PADOG

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


Bioconductor version: Release (3.19)

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 L. Tarca <atarca at med.wayne.edu>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")
PADOG PDF R Script
Reference Manual PDF

Details

biocViews Microarray, OneChannel, Software, TwoChannel
Version 1.46.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL (>= 2)
Depends R (>= 3.0.0), KEGGdzPathwaysGEO, methods, Biobase
Imports limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme
System Requirements
URL
See More
Suggests doParallel, parallel
Linking To
Enhances
Depends On Me BLMA
Imports Me EGSEA
Suggests Me ReporterScore
Links To Me
Build Report Build Report

Package Archives

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

Source Package PADOG_1.46.0.tar.gz
Windows Binary PADOG_1.46.0.zip (64-bit only)
macOS Binary (x86_64) PADOG_1.46.0.tgz
macOS Binary (arm64) PADOG_1.46.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PADOG
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PADOG
Bioc Package Browser https://code.bioconductor.org/browse/PADOG/
Package Short Url https://bioconductor.org/packages/PADOG/
Package Downloads Report Download Stats