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Ensemble of Gene Set Enrichment Analyses

Bioconductor version: Release (3.19)

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set.

Author: Monther Alhamdoosh [aut, cre], Luyi Tian [aut], Milica Ng [aut], Matthew Ritchie [ctb]

Maintainer: Monther Alhamdoosh <m.hamdoosh at>

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


To install this package, start R (version "4.4") 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:

EGSEA vignette PDF R Script
Reference Manual PDF


biocViews Classification, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, GeneSignaling, GeneTarget, Genetics, GraphAndNetwork, ImmunoOncology, KEGG, Metabolomics, Microarray, MultipleComparison, Network, NetworkEnrichment, OneChannel, Pathways, Proteomics, RNASeq, Sequencing, Software, SystemsBiology, TwoChannel
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends R (>= 4.3.0), Biobase, gage(>= 2.14.4), AnnotationDbi, topGO(>= 2.16.0), pathview(>= 1.4.2)
Imports PADOG(>= 1.6.0), GSVA(>= 1.12.0), globaltest(>= 5.18.0), limma(>= 3.20.9), edgeR(>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe(>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils,,,, RColorBrewer, methods, EGSEAdata(>= 1.3.1), htmlwidgets, plotly, DT
System Requirements
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Suggests BiocStyle, knitr, testthat
Linking To
Depends On Me EGSEA123
Imports Me
Suggests Me tidybulk, EGSEAdata
Links To Me
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Package Archives

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

Source Package EGSEA_1.32.0.tar.gz
Windows Binary
macOS Binary (x86_64) EGSEA_1.32.0.tgz
macOS Binary (arm64) EGSEA_1.32.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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