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Bioconductor - multiGSEA

multiGSEA

This is the released version of multiGSEA; for the devel version, see multiGSEA.

Combining GSEA-based pathway enrichment with multi omics data integration

Bioconductor version: Release (3.21)

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] ORCID: 0000-0001-7935-9582 , Jörg Hackermüller [aut] ORCID: 0000-0003-4920-7072

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

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

To install this package, start R (version "4.5") 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")
Details biocViews BioCarta, GeneSetEnrichment, Pathways, Reactome, Software Version 1.18.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License GPL-3 Depends R (>= 4.0.0) Imports magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods System Requirements URL https://github.com/yigbt/multiGSEA Bug Reports https://github.com/yigbt/multiGSEA/issues See More 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) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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