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

Functions

adjMatrix Man page
analyzeNetwork Man page
clustersDistance Man page
fea2incidMat Man page
fea_david Man page
fea_gage Man page
fea_gtLinker Man page
fea_gtLinker_getResults Man page
FEA_tools Man page
fea_topGO Man page
FGNet Man page
FGNet_GUI Man page
FGNet-package Man page
FGNet_report Man page
format_david Man page
format_results Man page
functionalNetwork Man page
getResults_david Man page
getResults_gtLinker Man page
getTerms Man page
GOEvidenceCodes Man page
groupTypes Man page
intersectionNetwork Man page
keywordsTerm Man page
organisms Man page
plotGoAncestors Man page
plotKegg Man page
plotMetagroupsDistance Man page
query_david Man page
query_gtLinker Man page
readGeneTermSets Man page
report_david Man page
report_gtLinker Man page
toMatrix Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.