EGSEA

DOI: 10.18129/B9.bioc.EGSEA    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see EGSEA.

Ensemble of Gene Set Enrichment Analyses

Bioconductor version: 3.12

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.

Author: Monther Alhamdoosh, Luyi Tian, Milica Ng and Matthew Ritchie

Maintainer: Monther Alhamdoosh <m.hamdoosh at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	EGSEA vignette
PDF		Reference Manual
Text		NEWS

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	1.18.1
In Bioconductor since	BioC 3.3 (R-3.3) (5 years)
License	GPL-3
Depends	R (>= 3.5), 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), Glimma(>= 1.4.0), htmlwidgets, plotly, DT
LinkingTo
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me	EGSEA123
Imports Me
Suggests Me	EGSEAdata
Links To Me
Build Report

Package Archives

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

Source Package	EGSEA_1.18.1.tar.gz
Windows Binary	EGSEA_1.18.1.zip
macOS 10.13 (High Sierra)	EGSEA_1.18.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EGSEA
Source Repository (Developer Access)	git clone [email protected]:packages/EGSEA
Package Short Url	https://bioconductor.org/packages/EGSEA/
Package Downloads Report	Download Stats