Package: FGNet 3.47.0

Sara Aibar

FGNet: Functional Gene Networks derived from biological enrichment analyses

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.

Authors:Sara Aibar, Celia Fontanillo, Conrad Droste and Javier De Las Rivas.

FGNet_3.47.0.tar.gz
FGNet_3.47.0.zip(r-4.7)FGNet_3.47.0.zip(r-4.6)FGNet_3.47.0.zip(r-4.5)
FGNet_3.47.0.tgz(r-4.6-any)FGNet_3.47.0.tgz(r-4.5-any)
FGNet_3.47.0.tar.gz(r-4.7-any)FGNet_3.47.0.tar.gz(r-4.6-any)
FGNet_3.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FGNet/json (API)
NEWS

# Install 'FGNet' in R:

install.packages('FGNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

FEA_tools - FGNet data
GOEvidenceCodes - FGNet data
groupTypes - FGNet data
organisms - FGNet data

On BioConductor:FGNet-3.47.0(bioc 3.24)FGNet-3.46.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

annotation go pathways genesetenrichment network visualization functionalgenomics networkenrichment clustering

4.62 score 1 packages 5 scripts 443 downloads 7 mentions 16 exports 24 dependencies

Last updated from:b133ae0a21. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	206
linux-devel-x86_64	WARNING	260
source / vignettes	OK	258
linux-release-x86_64	WARNING	243
macos-release-arm64	WARNING	147
macos-oldrel-arm64	WARNING	170
windows-devel	WARNING	520
windows-release	WARNING	153
windows-oldrel	WARNING	433
wasm-release	OK	169

Exports:analyzeNetwork clustersDistance fea_gage fea_gtLinker fea_gtLinker_getResults fea_topGO fea2incidMat FGNet_GUI FGNet_report format_david format_results functionalNetwork getTerms keywordsTerm plotGoAncestors readGeneTermSets

Dependencies:cli cpp11 glue hwriter igraph lattice lifecycle magrittr Matrix pkgconfig plotrix plyr png R.methodsS3 R.oo R.utils RColorBrewer Rcpp reshape2 rlang stringi stringr vctrs XML

FGNet

Rendered fromFGNet.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-04-08
Started: 2014-10-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Functional gene networks derived from biological enrichment analyses	FGNet-package FGNet
Analyze Functional Network	analyzeNetwork
Plots distances between metagroups.	clustersDistance plotMetagroupsDistance
FEA - GAGE	fea_gage
FEA - Gene-Term Linker	fea_gtLinker fea_gtLinker_getResults getResults_gtLinker query_gtLinker
FEA - topGO	fea_topGO
Transforms FEA output into incidence matrices.	adjMatrix fea2incidMat toMatrix
FGNet graphical user interface	FGNet_GUI
FGNet report	FGNet_report report_david report_gtLinker
Format DAVID output	format_david getResults_david
Format FEA results from external tools.	format_results
Creates and plots the functional gene network.	functionalNetwork intersectionNetwork
Get terms in the metagroups/clusters.	getTerms
Select keyword term	keywordsTerm
FGNet data	FEA_tools GOEvidenceCodes groupTypes organisms
Plot GO term ancestors	plotGoAncestors
Read gene-term sets	readGeneTermSets