multiGSEA

DOI: 10.18129/B9.bioc.multiGSEA    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see multiGSEA.

Combining GSEA-based pathway enrichment with multi omics data integration

Bioconductor version: 3.14

Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

Author: Sebastian Canzler [aut, cre] , Jörg Hackermüller [aut]

Maintainer: Sebastian Canzler <sebastian.canzler at ufz.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("multiGSEA")

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("multiGSEA")

 

HTML	R Script	multiGSEA.html
PDF		Reference Manual
Text		NEWS

Details

biocViews	BioCarta, GeneSetEnrichment, Pathways, Reactome, Software
Version	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	magrittr, graphite, AnnotationDbi, dplyr, fgsea, metap, rappdirs, rlang, methods
LinkingTo
Suggests	org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, metaboliteIDmapping, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/yigbt/multiGSEA
BugReports	https://github.com/yigbt/multiGSEA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	multiGSEA_1.4.0.tar.gz
Windows Binary	multiGSEA_1.4.0.zip
macOS 10.13 (High Sierra)	multiGSEA_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/multiGSEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/multiGSEA
Package Short Url	https://bioconductor.org/packages/multiGSEA/
Package Downloads Report	Download Stats