FGNet: Functional Gene Networks derived from biological enrichment analyses
Version 3.10.0

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.

AuthorSara Aibar, Celia Fontanillo, Conrad Droste and Javier De Las Rivas.
Bioconductor views Annotation Clustering FunctionalGenomics GO GeneSetEnrichment Network NetworkEnrichment Pathways Visualization
Date of publicationNone
MaintainerSara Aibar <saibar@usal.es>
LicenseGPL (>= 2)
Version3.10.0
URL http://www.cicancer.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FGNet")

Getting started

Package overview
FGNet

Popular man pages

data: FGNet data
fea_gtLinker: FEA - Gene-Term Linker
fea_topGO: FEA - topGO
FGNet_GUI: FGNet graphical user interface
functionalNetwork: Creates and plots the functional gene network.
plotGoAncestors: Plot GO term ancestors
plotKegg: Plot KEGG pathway
See all...

All man pages Function index File listing

Man pages

analyzeNetwork: Analyze Functional Network
clustersDistance: Plots distances between metagroups.
data: FGNet data
fea2incidMat: Transforms FEA output into incidence matrices.
fea_david: FEA - DAVID
fea_gage: FEA - GAGE
fea_gtLinker: FEA - Gene-Term Linker
fea_topGO: FEA - topGO
FGNet_GUI: FGNet graphical user interface
FGNet-package: Functional gene networks derived from biological enrichment...
FGNet_report: FGNet report
format_david: Format DAVID output
format_results: Format FEA results from external tools.
functionalNetwork: Creates and plots the functional gene network.
getTerms: Get terms in the metagroups/clusters.
keywordsTerm: Select keyword term
plotGoAncestors: Plot GO term ancestors
plotKegg: Plot KEGG pathway
readGeneTermSets: Read gene-term sets

Functions

FEA_tools Man page
FGNet Man page
FGNet-package Man page
FGNet_GUI Man page Source code
FGNet_report Man page Source code
GOEvidenceCodes Man page
SOAPQuery Source code
actDeactGenes Source code
addGeneLabels Source code
adjMatrix Man page
analyzeNetwork Man page Source code
buildGeneSets Source code
buildTermsTable Source code
clDescriptions Source code
clustersDistance Man page Source code
clustersTable Source code
createHTML_FEA_header Source code
createHtml Source code
errorMsgDavid Source code
fea2incidMat Man page Source code
fea_david Man page Source code
fea_gage Man page Source code
fea_gtLinker Man page Source code
fea_gtLinker_getResults Man page Source code
fea_topGO Man page Source code
fillCombosColumns Source code
formatResultsFile Source code
formatTerms Source code
format_david Man page Source code
format_gtLinker Source code
format_results Man page Source code
functionalNetwork Man page Source code
generateNetwork Source code
generateReport Source code
getContent Source code
getJobName Source code
getMGTerms Source code
getResults_david Man page
getResults_gtLinker Man page
getTerms Man page Source code
goTreeLinks Source code
groupTypes Man page
intersectionNetwork Man page
keywordsTerm Man page Source code
loadEset Source code
loadFileDialog Source code
loadInstPkg Source code
newDavidVars Source code
organisms Man page
plotFGNet Source code
plotFGNet_bipartite Source code
plotFGNet_default Source code
plotGoAncestors Man page Source code
plotKegg Man page Source code
plotMetagroupsDistance Man page
plotSubNetwork Source code
processExpressionField Source code
processFile Source code
processGenesField Source code
queryArgsAsCharacter Source code
query_david Man page
query_gtLinker Man page
readFEAresults Source code
readGeneTermSets Man page Source code
refList Source code
report_david Man page
report_gtLinker Man page
selectAPI Source code
selectLoadGs Source code
selectNetworkTool Source code
selectNetworkType Source code
selectNewGs Source code
selectWs Source code
selectWs_fillFields Source code
setColors Source code
showVignette Source code
submitQuery Source code
syncTermDescCombos Source code
tabDavid_fill Source code
tabFEA_fill Source code
tabGTL_fill Source code
tabGage_fill Source code
tabHelp_fill Source code
tabNetwork_common_fill Source code
tabNetwork_fill Source code
tabOther_fill Source code
tabPlotNetwork_fill Source code
tabReport_fill Source code
tabSubNetwork_fill Source code
tabTopGo_fill Source code
toMatrix Man page
viewFile Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/0_FGNet_GUI.R
R/0_FGNet_report.R
R/1a_fea_david.R
R/1a_fea_gage.R
R/1a_fea_gtLinker.R
R/1a_fea_gtLinker_getResults.R
R/1a_fea_topGO.R
R/1b_format_david.R
R/1b_format_feaResults.R
R/1c_readGeneTermSets.R
R/2_fea2incidMat.R
R/3_analyzeNetwork.R
R/3_clustersDistance.R
R/3_functionalNetwork.R
R/GUI_auxFunctions.R
R/GUI_tabFEA.R
R/GUI_tabFEA_tabDavid.R
R/GUI_tabFEA_tabGage.R
R/GUI_tabFEA_tabGtLinker.R
R/GUI_tabFEA_tabOther.R
R/GUI_tabFEA_tabTopGO.R
R/GUI_tabHelp.R
R/GUI_tabNetwork.R
R/GUI_tabNetwork_common.R
R/GUI_tabNetwork_tabOnlyNw.R
R/GUI_tabNetwork_tabReport.R
R/GUI_tabNetwork_tabSubNw.R
R/getTerms.R
R/keyWordsTerm.R
R/plotGoAncestors.R
R/plotKegg.R
R/plotSubNetwork.R
R/private_SOAPquery.R
R/private_addGeneLabels.R
R/private_buildGeneSets.R
R/private_clustersTable.R
R/private_createHTML_FEA_header.R
R/private_createHtml.R
R/private_getJobName.R
R/private_getMGTerms.R
R/private_loadInstPkg.R
R/private_plotFGNet.R
R/private_plotFGNet_bipartite.R
R/private_plotFGNet_default.R
R/private_queryArgsAsCharacter.R
R/private_setColors.R
build
build/vignette.rds
data
data/FEA_tools.RData
data/GOEvidenceCodes.RData
data/datalist
data/groupTypes.RData
data/organisms.RData
inst
inst/CITATION
inst/css
inst/css/functionalNetworks.css
inst/doc
inst/doc/FGNet.R
inst/doc/FGNet.Rmd
inst/doc/FGNet.html
inst/examples
inst/examples/DAVID_Yeast_overl6_raw.txt
inst/examples/DAVID_Yeast_raw.txt
inst/unitTests
inst/unitTests/test_getResults_david.R
inst/unitTests/test_getResults_gtLinker.R
man
man/FGNet-package.Rd
man/FGNet_GUI.Rd
man/FGNet_report.Rd
man/analyzeNetwork.Rd
man/clustersDistance.Rd
man/data.Rd
man/fea2incidMat.Rd
man/fea_david.Rd
man/fea_gage.Rd
man/fea_gtLinker.Rd
man/fea_topGO.Rd
man/format_david.Rd
man/format_results.Rd
man/functionalNetwork.Rd
man/getTerms.Rd
man/keywordsTerm.Rd
man/plotGoAncestors.Rd
man/plotKegg.Rd
man/readGeneTermSets.Rd
tests
tests/runTests.R
vignettes
vignettes/FGNet.Rmd
vignettes/FGNet_GUI.png
vignettes/FGNet_workflow.png
vignettes/TermsYeast.png
vignettes/hsa05010_Alzheimer_disease.png
vignettes/nwExample1.png
vignettes/nwExample2.png
vignettes/nwExample3.png
vignettes/ssDavid.png
vignettes/ssGtlinker.png
FGNet documentation built on May 20, 2017, 11 p.m.

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