Package: multiGSEA 1.17.2

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_1.17.2.tar.gz
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multiGSEA.pdf |multiGSEA.html
multiGSEA/json (API)
NEWS

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

Peer review:

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-1.17.0(bioc 3.21)multiGSEA-1.16.0(bioc 3.20)

genesetenrichmentpathwaysreactomebiocarta

6.92 score 17 stars 28 scripts 282 downloads 1 mentions 11 exports 113 dependencies

Last updated 27 days agofrom:6def494cfe. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 26 2024
R-4.5-winOKNov 26 2024
R-4.5-linuxOKNov 26 2024
R-4.4-winOKNov 26 2024
R-4.4-macOKNov 26 2024
R-4.3-winOKNov 26 2024
R-4.3-macOKNov 26 2024

Exports:combinePvaluesextractPvaluesgetFeaturesgetGeneMappinggetMetaboliteMappinggetMultiOmicsFeaturesgetOrganismsinitOmicsDataStructuremultiGSEArankFeaturesrename_duplicates

Dependencies:AnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobcachemclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDEoptimRdplyrfansifarverfastmapfastmatchfgseafilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegraphgraphitegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSmathjaxrMatrixMatrixModelsmemoisemetaboliteIDmappingmetapmgcvmimemnormtmultcompmulttestmunsellmutossmvtnormnlmenumDerivopensslpillarpkgconfigplogrplotrixpngpurrrqqconfquantregR6rappdirsrbibutilsRColorBrewerRcppRdpackrlangrobustbaseRSQLiteS4VectorssandwichscalessnsnowSparseMstringistringrsurvivalsysTFisherTH.datatibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectoryamlzlibbioczoo

multiGSEA: an example workflow

Rendered frommultiGSEA.rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-04-08
Started: 2020-04-05