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FGNet

Functional Gene Networks derived from biological enrichment analyses

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("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")
FGNet HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Clustering, FunctionalGenomics, GO, GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software, Visualization
Version 3.34.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License GPL (>= 2)
Depends R (>= 4.2.0)
Imports igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices
Linking To
Suggests RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager
System Requirements
Enhances
URL http://www.cicancer.org
See More
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_3.34.0.tar.gz
Windows Binary FGNet_3.34.0.zip
macOS Binary (x86_64) FGNet_3.34.0.tgz
macOS Binary (arm64) FGNet_3.34.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FGNet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FGNet
Bioc Package Browser https://code.bioconductor.org/browse/FGNet/
Package Short Url https://bioconductor.org/packages/FGNet/
Package Downloads Report Download Stats