Package: PADOG 1.55.1

Adi L. Tarca

PADOG: Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that appear 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 42 datasets originally curated in KEGGdzPathwaysGEO and KEGGandMetacoreDzPathwaysGEO data packages.

Authors:Adi Laurentiu Tarca <[email protected]>; Zhonghui Xu <[email protected]>; Gaurav Bhatti <[email protected]>

PADOG_1.55.1.tar.gz
PADOG_1.55.1.zip(r-4.7-any)PADOG_1.55.1.zip(r-4.6-any)PADOG_1.55.1.zip(r-4.5-any)
PADOG_1.55.1.tgz(r-4.6-any)PADOG_1.55.1.tgz(r-4.5-any)
PADOG_1.55.1.tar.gz(r-4.7-any)PADOG_1.55.1.tar.gz(r-4.6-any)
PADOG_1.55.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PADOG/json (API)

# Install 'PADOG' in R:

install.packages('PADOG', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:PADOG-1.55.0(bioc 3.24)PADOG-1.54.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray onechannel twochannel

5.79 score 3 packages 23 scripts 846 downloads 19 mentions 4 exports 50 dependencies

Last updated from:dbc3d6fd21. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	190
linux-devel	NOTE	390
source / vignettes	OK	312
linux-release	NOTE	390
macos-release	NOTE	270
macos-oldrel	NOTE	269
windows-devel	NOTE	279
windows-release	NOTE	283
windows-oldrel	NOTE	233
wasm-release	OK	156

Exports:compPADOG filteranot loadCompPADOGBenchmark padog

Dependencies:AnnotationDbi askpass Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI digest doRNG fastmap foreach generics glue GSA hgu133a.db hgu133plus2.db httr IRanges iterators jsonlite KEGGREST lattice lifecycle limma memoise mime nlme openssl org.Hs.eg.db pkgconfig png R6 rlang rngtools RSQLite S4Vectors Seqinfo statmod sys vctrs XVector

PADOG

Overview | Pathway / gene set analysis with PADOG package | Benchmark of gene set analysis methods | Changes in version 1.6

Rendered fromPADOG.Rnwusingutils::Sweave

Last update: 2026-10-19
Started: 2013-11-01

Help page	Topics
Benchmark for gene set analysis methods introduced by Tarca et al. in the PADOG package	compPADOG
Remove duplicate probesets/probes from an gene expression matrix based on p-values from a moderated t-test, in order to apply a gene set analysis.	filteranot
Benchmark for gene set analysis methods	loadCompPADOGBenchmark
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)	padog

Package: PADOG 1.55.1

PADOG: Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

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