FGNet

DOI: 10.18129/B9.bioc.FGNet    

Functional Gene Networks derived from biological enrichment analyses

Bioconductor version: Release (3.13)

Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.

Author: Sara Aibar, Celia Fontanillo, Conrad Droste and Javier De Las Rivas.

Maintainer: Sara Aibar <saibar at usal.es>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("FGNet")

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("FGNet")

 

HTML	R Script	FGNet
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Clustering, FunctionalGenomics, GO, GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software, Visualization
Version	3.26.0
In Bioconductor since	BioC 2.13 (R-3.0) (8 years)
License	GPL (>= 2)
Depends	R (>= 2.15)
Imports	igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices
LinkingTo
Suggests	RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, RGtk2, BiocManager
SystemRequirements
Enhances
URL	http://www.cicancer.org
Depends On Me
Imports Me	IntramiRExploreR
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	FGNet_3.26.0.tar.gz
Windows Binary	FGNet_3.26.0.zip
macOS 10.13 (High Sierra)	FGNet_3.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FGNet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FGNet
Package Short Url	https://bioconductor.org/packages/FGNet/
Package Downloads Report	Download Stats