FGNet

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see FGNet.

Functional Gene Networks derived from biological enrichment analyses

Bioconductor version: 3.15

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Clustering, FunctionalGenomics, GO, GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software, Visualization

Version 3.30.0

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

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

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Build Report Build Report

Package Archives

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

Source Package FGNet_3.30.0.tar.gz

Windows Binary FGNet_3.30.0.zip

macOS Binary (x86_64) FGNet_3.30.0.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

Old Source Packages for BioC 3.15 Source Archive