Package: PADOG 1.55.0

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 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.

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

PADOG_1.55.0.tar.gz
PADOG_1.55.0.zip(r-4.7)PADOG_1.55.0.zip(r-4.6)PADOG_1.55.0.zip(r-4.5)
PADOG_1.55.0.tgz(r-4.6-any)PADOG_1.55.0.tgz(r-4.5-any)
PADOG_1.55.0.tar.gz(r-4.7-any)PADOG_1.55.0.tar.gz(r-4.6-any)
PADOG_1.55.0.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

5.31 score 2 packages 17 scripts 19 mentions 3 exports 50 dependencies

Last updated from:8d85cf2b04. Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	FAILURE	222
linux-devel-x86_64	NOTE	313
source / vignettes	OK	361
linux-release-x86_64	NOTE	288
macos-release-arm64	NOTE	259
macos-oldrel-arm64	NOTE	221
windows-devel	NOTE	235
windows-release	NOTE	218
windows-oldrel	NOTE	271
wasm-release	OK	159

Exports:compPADOG filteranot padog

Dependencies:AnnotationDbi askpass Biobase 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 KEGGdzPathwaysGEO 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

Rendered fromPADOG.Rnwusingutils::Sweave

Last update: 2023-11-04
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Benchmark for gene set analysis methods using 24 datasets	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
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)	padog