FGNet: Functional Gene Networks derived from biological enrichment analyses

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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.
Date of publication
None
Maintainer
Sara Aibar <saibar@usal.es>
License
GPL (>= 2)
Version
3.8.0
URLs

View on Bioconductor

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

Files in this package

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