Package: RTopper 1.59.0

Luigi Marchionni

RTopper: This package is designed to perform Gene Set Analysis across multiple genomic platforms

the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms.

Authors:Luigi Marchionni <[email protected]>, Svitlana Tyekucheva <[email protected]>

# Install 'RTopper' in R:

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

Datasets:

dat - A test dataset for the RTopper package
fgsList - A list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package
gseResultsSep - A list of separated gene set enrichment p-values to be used to run the examples in the RTopper package
intScores - A list of genomic scores integrated across distinct data sets to be used to run the examples in the RTopper package
pheno - A test dataset for the RTopper package
sepScores - A list of separate gene-to-phenotype association scores, obtained indipendently for each distinct data set to be used to run the examples in the RTopper package

On BioConductor:RTopper-1.59.0(bioc 3.24)RTopper-1.58.0(bioc 3.23)

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

Last updated from:41b97ec495. Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	166
linux-devel-x86_64	WARNING	238
source / vignettes	ERROR	462
linux-release-x86_64	WARNING	231
macos-release-arm64	WARNING	116
macos-oldrel-arm64	WARNING	162
windows-devel	WARNING	412
windows-release	WARNING	380
windows-oldrel	WARNING	379
wasm-release	OK	136

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
A package to perform run Gene Set Enrichment across genomic platforms	RTopper-package RTopper
Multiple testing correction	adjustPvalGSE
Combines GSE results	combineGSE
Computes gene-to-phenotype associations scores	computeDrStat
Converts genomic data to a list suitable for computing gene-to-phenotype scores	convertToDr
A test dataset for the RTopper package	dat
A list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package	fgsList
A list of separated gene set enrichment p-values to be used to run the examples in the RTopper package	gseResultsSep
A list of genomic scores integrated across distinct data sets to be used to run the examples in the RTopper package	intScores
A test dataset for the RTopper package	pheno
To perform GSE analysis over multipple experiments and functional themes	runBatchGSE
A list of separate gene-to-phenotype association scores, obtained indipendently for each distinct data set to be used to run the examples in the RTopper package	sepScores