FGNet
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see FGNet.
Functional Gene Networks derived from biological enrichment analyses
Bioconductor version: 3.10
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("FGNet")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, FunctionalGenomics, GO, GeneSetEnrichment, Network, NetworkEnrichment, Pathways, Software, Visualization |
| Version | 3.20.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15) |
| Imports | igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png |
| System Requirements | |
| URL | http://www.cicancer.org |
See More
| Suggests | RCurl, RDAVIDWebService, gage, topGO, GO.db, KEGG.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, RGtk2, 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_3.20.0.tar.gz |
| Windows Binary | FGNet_3.20.0.zip |
| Mac OS X 10.11 (El Capitan) | FGNet_3.20.0.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 3.10 | Source Archive |