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EGSEA

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

Ensemble of Gene Set Enrichment Analyses

Bioconductor version: Development (3.18)

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 "4.3") 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

Reference Manual PDF

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 1.29.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 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
Linking To
Suggests BiocStyle, knitr, testthat
System Requirements
Enhances
URL
See More
Depends On Me EGSEA123
Imports Me
Suggests Me EGSEAdata, tidybulk
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary EGSEA_1.29.0.zip (64-bit only)
macOS Binary (x86_64) EGSEA_1.29.0.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/
Package Downloads Report Download Stats