PADOG
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see PADOG.
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Bioconductor version: 3.8
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("PADOG")):
Installation
To install this package, start R (version "3.5") 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 | R Script | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Software, TwoChannel |
| Version | 1.24.0 |
| 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, KEGG.db, nlme |
| System Requirements | |
| URL |
See More
| Suggests | doParallel, parallel |
| Linking To | |
| Enhances | |
| Depends On Me | BLMA |
| Imports Me | EGSEA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PADOG_1.24.0.tar.gz |
| Windows Binary | PADOG_1.24.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | PADOG_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PADOG |
| Source Repository (Developer Access) | git clone [email protected]:packages/PADOG |
| Bioc Package Browser | https://code.bioconductor.org/browse/PADOG/ |
| Package Short Url | https://bioconductor.org/packages/PADOG/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |