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FGNet

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

Functional Gene Networks derived from biological enrichment analyses


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

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

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 3.37.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 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
System Requirements
URL http://www.cicancer.org
See More
Suggests RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager
Linking To
Enhances
Depends On Me
Imports Me IntramiRExploreR
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package FGNet_3.37.0.tar.gz
Windows Binary FGNet_3.37.0.zip (64-bit only)
macOS Binary (x86_64) FGNet_3.37.0.tgz
macOS Binary (arm64) FGNet_3.37.0.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