FGNet

DOI: 10.18129/B9.bioc.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 (3.11)

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script FGNet
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Clustering, FunctionalGenomics, GO, GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software, Visualization
Version 3.21.0
In Bioconductor since BioC 2.13 (R-3.0) (6 years)
License GPL (>= 2)
Depends R (>= 2.15)
Imports igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png
LinkingTo
Suggests RCurl, RDAVIDWebService, gage, topGO, GO.db, KEGG.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_3.21.0.tar.gz
Windows Binary FGNet_3.21.0.zip
Mac OS X 10.11 (El Capitan)
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

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