neaGUI: An R package to perform the network enrichment analysis (NEA).

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neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko et al. (2012). The NEA method extends the overlap statistics in GSEA to network links between genes in the experimental set and those in the functional categories by exploiting biological information in terms of gene interaction network. The neaGUI requires the following R packages: tcltk, KEGG.db, GO.db, reactome.db, org.Hs.eg.db, AnnotationDbi, and hwriter.

Author
Setia Pramana, Woojoo Lee, Yudi Pawitan
Date of publication
None
Maintainer
Setia Pramana <setia.pramana@ki.se>
License
GPL-2
Version
1.9.0

View on Bioconductor

Man pages

nea
Network Enrichment Analysis
neaGUI
neaGUI
neaGUI-package
IsoGeneGUI Graphical User Interface for the IsoGene package

Files in this package

neaGUI/DESCRIPTION
neaGUI/NAMESPACE
neaGUI/R
neaGUI/R/LoadRdata.R
neaGUI/R/arr2list.R
neaGUI/R/checkFgs.R
neaGUI/R/checkObject.R
neaGUI/R/countcon.R
neaGUI/R/gea.R
neaGUI/R/getAgs.R
neaGUI/R/getDb.R
neaGUI/R/getFGS.R
neaGUI/R/getNtw.R
neaGUI/R/getPnet.R
neaGUI/R/linknum.R
neaGUI/R/linknum.arr.R
neaGUI/R/linknum.arr.csum.R
neaGUI/R/linknum.list.R
neaGUI/R/linknum.list.csum.R
neaGUI/R/list2arr.R
neaGUI/R/list2arr0.R
neaGUI/R/manypnet.R
neaGUI/R/nea.R
neaGUI/R/neaGUI.R
neaGUI/R/neaMod.R
neaGUI/R/netperm.R
neaGUI/R/pval2FDR.R
neaGUI/R/resample.R
neaGUI/R/saveHtml.R
neaGUI/R/savingRes.R
neaGUI/R/savingRwd.R
neaGUI/R/test_neaGUI_package.R
neaGUI/R/zstat.R
neaGUI/build
neaGUI/build/vignette.rds
neaGUI/inst
neaGUI/inst/doc
neaGUI/inst/doc/neaGUI_vignette.R
neaGUI/inst/doc/neaGUI_vignette.Rnw
neaGUI/inst/doc/neaGUI_vignette.pdf
neaGUI/inst/extdata
neaGUI/inst/extdata/AGS.csv
neaGUI/inst/extdata/AGSnea.txt
neaGUI/inst/extdata/NETWORK.csv
neaGUI/inst/extdata/example.RData
neaGUI/inst/extdata/network.txt
neaGUI/inst/images
neaGUI/inst/images/AGScsv.jpg
neaGUI/inst/images/AGStxt.jpg
neaGUI/inst/images/htmlout.jpg
neaGUI/inst/images/mainwin.jpg
neaGUI/inst/images/netwrkcsv.jpg
neaGUI/inst/images/netwrktxt.jpg
neaGUI/inst/images/rdinput.jpg
neaGUI/inst/index.html
neaGUI/inst/input.html
neaGUI/inst/mainWin.html
neaGUI/inst/output.html
neaGUI/inst/unitTests
neaGUI/inst/unitTests/Runitest.R
neaGUI/inst/unitTests/runitneaGUI.R
neaGUI/man
neaGUI/man/nea.Rd
neaGUI/man/neaGUI-package.Rd
neaGUI/man/neaGUI.Rd
neaGUI/tests
neaGUI/tests/neagui_unit_tests.R
neaGUI/vignettes
neaGUI/vignettes/images
neaGUI/vignettes/images/htmlout.jpg
neaGUI/vignettes/images/neawin2.jpg
neaGUI/vignettes/neaGUI_vignette.Rnw