gsean

DOI: 10.18129/B9.bioc.gsean    

Gene Set Enrichment Analysis with Networks

Bioconductor version: Release (3.7)

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gsean")

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

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod
Version 1.0.0
License Artistic-2.0
Depends R (>= 3.5), fgsea, PPInfer
Imports
LinkingTo
Suggests DESeq2, knitr, plotly, RANKS, WGCNA
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package gsean_1.0.0.tar.gz
Windows Binary gsean_1.0.0.zip
Mac OS X 10.11 (El Capitan) gsean_1.0.0.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 http://bioconductor.org/packages/gsean/
Package Downloads Report Download Stats

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