EGSEA

DOI: 10.18129/B9.bioc.EGSEA    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see EGSEA.

Ensemble of Gene Set Enrichment Analyses

Bioconductor version: 3.15

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 "4.2") 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")

 

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 1.24.0
In Bioconductor since BioC 3.3 (R-3.3) (6.5 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), 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_1.24.0.tar.gz
Windows Binary EGSEA_1.24.0.zip
macOS Binary (x86_64) EGSEA_1.24.0.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

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