FGNet

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

Functional Gene Networks derived from biological enrichment analyses

Bioconductor version: Development (3.24)

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")):

Sara Aibar, Celia Fontanillo, Conrad Droste and Javier De Las Rivas. FGNet: Functional Gene Networks derived from biological enrichment analyses. doi:10.18129/B9.bioc.FGNet, R package version 3.47.0, https://bioconductor.org/packages/FGNet.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Clustering, FunctionalGenomics, GO, GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software, Visualization
Version	3.47.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 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

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, r-universe

Package Archives

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

Source Package	FGNet_3.47.0.tar.gz
Windows Binary (x86_64)	FGNet_3.47.0.zip
macOS Binary (big-sur-x86_64)	FGNet_3.47.0.tgz
macOS Binary (sonoma-arm64)	FGNet_3.47.0.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