EGSEA

This is the released version of EGSEA; for the devel version, see EGSEA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Ensemble of Gene Set Enrichment Analyses

Bioconductor version: Release (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")):

Monther Alhamdoosh, Luyi Tian, Milica Ng. EGSEA: Ensemble of Gene Set Enrichment Analyses. doi:10.18129/B9.bioc.EGSEA, R package version 1.40.0, https://bioconductor.org/packages/EGSEA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

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	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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	EGSEAdata, tidybulk
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	EGSEA_1.40.0.tar.gz
Windows Binary (x86_64)	EGSEA_1.40.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	EGSEA_1.40.0.tgz
macOS Binary (sonoma-arm64)	EGSEA_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EGSEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EGSEA
Package Short Url	https://bioconductor.org/packages/EGSEA/
Package Downloads Report	Download Stats