PADOG
This is the released version of PADOG; for the devel version, see PADOG.
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Bioconductor version: Release (3.23)
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("PADOG")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.54.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 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_1.54.0.tar.gz |
| Windows Binary (x86_64) | PADOG_1.54.0.zip |
| macOS Binary (big-sur-x86_64) | PADOG_1.54.0.tgz |
| macOS Binary (sonoma-arm64) | PADOG_1.54.0.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 |