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Reproducible GSEA Benchmarking

Bioconductor version: Release (3.18)

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.

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

Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Reproducible GSEA Benchmarking HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Microarray, Network, NetworkEnrichment, Pathways, RNASeq, ReportWriting, Software, Visualization
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5.0), Biobase, SummarizedExperiment
Imports AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils
System Requirements
URL https://github.com/waldronlab/GSEABenchmarkeR
Bug Reports https://github.com/waldronlab/GSEABenchmarkeR/issues
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Suggests BiocStyle, GSE62944, knitr, rappdirs, rmarkdown
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Package Archives

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

Source Package GSEABenchmarkeR_1.22.0.tar.gz
Windows Binary GSEABenchmarkeR_1.22.0.zip
macOS Binary (x86_64) GSEABenchmarkeR_1.22.0.tgz
macOS Binary (arm64) GSEABenchmarkeR_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GSEABenchmarkeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GSEABenchmarkeR
Bioc Package Browser https://code.bioconductor.org/browse/GSEABenchmarkeR/
Package Short Url https://bioconductor.org/packages/GSEABenchmarkeR/
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