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gsean

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

Gene Set Enrichment Analysis with Networks


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
gsean HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5), fgsea, PPInfer
Imports
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URL
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Suggests SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown
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Package Archives

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

Source Package gsean_1.23.0.tar.gz
Windows Binary
macOS Binary (x86_64) gsean_1.23.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/gsean
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gsean
Bioc Package Browser https://code.bioconductor.org/browse/gsean/
Package Short Url https://bioconductor.org/packages/gsean/
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