Package: GSEABenchmarkeR 1.27.0

Ludwig Geistlinger

GSEABenchmarkeR: Reproducible GSEA Benchmarking

The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.

Authors:Ludwig Geistlinger [aut, cre], Gergely Csaba [aut], Mara Santarelli [ctb], Lucas Schiffer [ctb], Marcel Ramos [ctb], Ralf Zimmer [aut], Levi Waldron [aut]

GSEABenchmarkeR_1.27.0.tar.gz
GSEABenchmarkeR_1.27.0.zip(r-4.5)GSEABenchmarkeR_1.27.0.zip(r-4.4)GSEABenchmarkeR_1.27.0.zip(r-4.3)
GSEABenchmarkeR_1.27.0.tgz(r-4.5-any)GSEABenchmarkeR_1.27.0.tgz(r-4.4-any)GSEABenchmarkeR_1.27.0.tgz(r-4.3-any)
GSEABenchmarkeR_1.27.0.tar.gz(r-4.5-noble)GSEABenchmarkeR_1.27.0.tar.gz(r-4.4-noble)
GSEABenchmarkeR_1.27.0.tgz(r-4.4-emscripten)GSEABenchmarkeR_1.27.0.tgz(r-4.3-emscripten)
GSEABenchmarkeR.pdf |GSEABenchmarkeR.html
GSEABenchmarkeR/json (API)
NEWS

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

Bug tracker:https://github.com/waldronlab/gseabenchmarker/issues

On BioConductor:GSEABenchmarkeR-1.27.0(bioc 3.21)GSEABenchmarkeR-1.26.0(bioc 3.20)

immunooncologymicroarrayrnaseqgeneexpressiondifferentialexpressionpathwaysgraphandnetworknetworkgenesetenrichmentnetworkenrichmentvisualizationreportwritingbioconductor-packageu24ca289073

6.55 score 13 stars 23 scripts 315 downloads 2 mentions 19 exports 101 dependencies

Last updated 5 months agofrom:7fc44fcb7f. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winNOTEMar 29 2025
R-4.5-macNOTEMar 29 2025
R-4.5-linuxNOTEMar 29 2025
R-4.4-winNOTEMar 29 2025
R-4.4-macNOTEMar 29 2025
R-4.4-linuxNOTEMar 29 2025
R-4.3-winNOTEMar 29 2025
R-4.3-macNOTEMar 29 2025

Exports:bpPlotcacheResourcecompOptcompRandevalNrSetsevalNrSigSetsevalRandomGSevalRelevanceevalTypeIErrorloadEDatamaPreprocmetaFCplotDEDistributionplotNrSamplesreadDataId2diseaseCodeMapreadResultsrunDErunEAwriteDE

Dependencies:abindannotateAnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyredgeREnrichmentBrowserExperimentHubfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueGO.dbgraphgraphiteGSEABasehttrhwriterIRangesjsonliteKEGGandMetacoreDzPathwaysGEOKEGGdzPathwaysGEOKEGGgraphKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpathviewpillarpkgconfigplogrpngpurrrR6rappdirsRCurlRgraphvizrlangRSQLiteS4ArraysS4VectorssafesnowSparseArraySparseMSPIAstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxtableXVectoryaml

Reproducible GSEA Benchmarking

Rendered fromGSEABenchmarkeR.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2021-06-05
Started: 2018-01-19