gsean

DOI: 10.18129/B9.bioc.gsean    

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

Gene Set Enrichment Analysis with Networks

Bioconductor version: 3.9

Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.

Author: Dongmin Jung

Maintainer: Dongmin Jung <dmdmjung at gmail.com>

Installation

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

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

BiocManager::install("gsean")

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("gsean")

 

HTML	R Script	gsean
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod
Version	1.4.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), fgsea, PPInfer
Imports
LinkingTo
Suggests	SummarizedExperiment, knitr, plotly, RANKS, WGCNA
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	gsean_1.4.0.tar.gz
Windows Binary	gsean_1.4.0.zip
Mac OS X 10.11 (El Capitan)	gsean_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gsean
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gsean
Package Short Url	https://bioconductor.org/packages/gsean/
Package Downloads Report	Download Stats