EGSEA

This is the development version of EGSEA; for the stable release version, see EGSEA.

Ensemble of Gene Set Enrichment Analyses

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DOI: 10.18129/B9.bioc.EGSEA

Bioconductor version: Development (3.23)

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 gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("EGSEA")

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

Documentation

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

browseVignettes("EGSEA")

EGSEA vignette PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

Version 1.39.0

In Bioconductor since BioC 3.3 (R-3.3) (9.5 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, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata(>= 1.3.1), htmlwidgets, plotly, DT

System Requirements

URL

Suggests BiocStyle, knitr, testthat

Linking To

Enhances

Depends On Me EGSEA123

Imports Me

Suggests Me tidybulk, EGSEAdata

Links To Me

Build Report Build Report

Package Archives

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

Source Package EGSEA_1.39.0.tar.gz

Windows Binary (x86_64) EGSEA_1.39.0.zip

macOS Binary (x86_64) EGSEA_1.39.0.tgz

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/EGSEA

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EGSEA

Bioc Package Browser https://code.bioconductor.org/browse/EGSEA/

Package Short Url https://bioconductor.org/packages/EGSEA/

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