PADOG
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Bioconductor version: Release (2.12)
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
| R Script | PADOG | |
| Reference Manual |
Details
| biocViews | Bioinformatics, Microarray, OneChannel, Software, TwoChannel |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.11 (R-2.16) |
| 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_1.2.0.tar.gz |
| Windows Binary | PADOG_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | PADOG_1.2.0.tgz |
| Package Downloads Report | Download Stats |
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