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.

AuthorSara Aibar, Celia Fontanillo, Conrad Droste and Javier De Las Rivas.
Date of publicationNone
MaintainerSara Aibar <saibar@usal.es>
LicenseGPL (>= 2)
Version3.8.0
http://www.cicancer.org

View on Bioconductor

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

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