Package: multiGSEA 1.23.0

Sebastian Canzler

multiGSEA: Combining GSEA-based pathway enrichment with multi omics data integration

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.

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

multiGSEA_1.23.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
multiGSEA/json (API)
NEWS

# Install 'multiGSEA' in R:
install.packages('multiGSEA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yigbt/multigsea/issues

Datasets:
  • metabolome - Metabolomic data set that is used in the toy example provided by the 'multiGSEA' package.
  • proteome - Proteomic data set that is used in the toy example provided by the 'multiGSEA' package.
  • transcriptome - Transcriptomic data set that is used in the toy example provided by the 'multiGSEA' package.

On BioConductor:multiGSEA-1.23.0(bioc 3.24)multiGSEA-1.22.0(bioc 3.23)

genesetenrichmentpathwaysreactomebiocarta

6.63 score 21 stars 41 scripts 416 downloads 1 mentions 11 exports 108 dependencies

Last updated from:1d8d9841f8. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE395
linux-devel-x86_64OK914
source / vignettesOK1214
linux-release-x86_64OK941
macos-release-arm64OK712
macos-oldrel-arm64OK494
windows-develOK1686
windows-releaseOK1639
windows-oldrelOK1463
wasm-releaseOK359

Exports:combinePvaluesextractPvaluesgetFeaturesgetGeneMappinggetMetaboliteMappinggetMultiOmicsFeaturesgetOrganismsinitOmicsDataStructuremultiGSEArankFeaturesrename_duplicates

Dependencies:AnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobcachemclicodetoolscowplotcpp11crayoncurldata.tableDBIdbplyrDEoptimRdir.expirydplyrfarverfastmapfastmatchfgseafilelockformatRfutile.loggerfutile.optionsgenericsggplot2gluegraphgraphitegtablehttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSmathjaxrMatrixMatrixModelsmemoisemetaboliteIDmappingmetapmimemnormtmultcompmulttestmutossmvtnormnumDerivopensslpillarpkgconfigplotrixpngpurrrqqconfquantregR6rappdirsrbibutilsRColorBrewerRcppRdpackrlangrobustbaseRSQLiteS4VectorsS7sandwichscalesSeqinfosnsnowSparseMstringistringrsurvivalsysTFisherTH.datatibbletidyrtidyselectutf8vctrsviridisLitewithrXVectoryamlzoo

multiGSEA: an example workflow

Sebastian Canzler, Jörg Hackermüller

Rendered frommultiGSEA.rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-01-06
Started: 2020-04-05