PADOG
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Bioconductor version: 3.23 · Package version: 1.54.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PADOG")Details
| Maintainer | Adi L. Tarca <atarca@med.wayne.edu> |
| Author | Adi Laurentiu Tarca <atarca@med.wayne.edu>; Zhonghui Xu <zhonghui.xu@gmail.com> |
| License | GPL (>= 2) |
| Downloads rank | 711 |
| Source branch | RELEASE_3_23 |
| biocViews | Microarray, OneChannel, Software, TwoChannel |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PADOG_1.54.0.tar.gz |
| Windows binary (x86_64) | PADOG_1.54.0.zip |
| macOS binary (arm64) | PADOG_1.54.0.tgz |
| macOS binary (x86_64) | PADOG_1.54.0.tgz |
Dependencies
Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods, Biobase
Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme
Suggests: doParallel, parallel