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multiGSEA

Combining GSEA-based pathway enrichment with multi omics data integration

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("multiGSEA")):

Installation

To install this package, start R (version "4.3") 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")
multiGSEA.html HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BioCarta, GeneSetEnrichment, Pathways, Reactome, Software
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.0.0)
Imports magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods
Linking To
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, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0)
System Requirements
Enhances
URL https://github.com/yigbt/multiGSEA
Bug Reports https://github.com/yigbt/multiGSEA/issues
See More
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_1.10.0.tar.gz
Windows Binary multiGSEA_1.10.0.zip
macOS Binary (x86_64) multiGSEA_1.10.0.tgz
macOS Binary (arm64) multiGSEA_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/multiGSEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/multiGSEA
Bioc Package Browser https://code.bioconductor.org/browse/multiGSEA/
Package Short Url https://bioconductor.org/packages/multiGSEA/
Package Downloads Report Download Stats