EGSEA

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see EGSEA.

Ensemble of Gene Set Enrichment Analyses


Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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

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 1.12.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL
See More
Suggests BiocStyle, knitr, testthat
Linking To
Enhances
Depends On Me EGSEA123
Imports Me
Suggests Me EGSEAdata
Links To Me
Build Report Build Report

Package Archives

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

Source Package EGSEA_1.12.0.tar.gz
Windows Binary EGSEA_1.12.0.zip
Mac OS X 10.11 (El Capitan) EGSEA_1.12.0.tgz
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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive