Package: FGNet 3.39.0

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_3.39.0.tar.gz
FGNet_3.39.0.zip(r-4.5)FGNet_3.39.0.zip(r-4.4)FGNet_3.39.0.zip(r-4.3)
FGNet_3.39.0.tgz(r-4.4-any)FGNet_3.39.0.tgz(r-4.3-any)
FGNet_3.39.0.tar.gz(r-4.5-noble)FGNet_3.39.0.tar.gz(r-4.4-noble)
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FGNet.pdf |FGNet.html✨
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-3.39.0(bioc 3.20)FGNet-3.38.0(bioc 3.19)

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

bioconductor-package

16 exports 2.35 score 24 dependencies 1 dependents 7 mentions

Last updated 2 months agofrom:b55312ada5

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 Jul 03 2024.

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