To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PADOG")
In most cases, you don't need to download the package archive at all.
PADOG
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see PADOG.
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Bioconductor version: 3.4
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:
## try http:// if https:// URLs are not supported
source("https://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")
| R Script | PADOG | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Software, TwoChannel |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (4.5 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 | EGSEA |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PADOG_1.16.0.tar.gz |
| Windows Binary | PADOG_1.16.0.zip |
| Mac OS X 10.9 (Mavericks) | PADOG_1.16.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/PADOG/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/PADOG/ |
| Package Downloads Report | Download Stats |
Documentation »
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