neaGUI: A user friendly 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
Date of publication
2013-08-20 20:43:14
Maintainer
setia pramana <setia.pramana@ki.se>
License
GPL-2
Version
0.99.0

View on R-Forge

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/inst
neaGUI/inst/doc
neaGUI/inst/doc/images
neaGUI/inst/doc/images/htmlout.jpg
neaGUI/inst/doc/images/neawin2.jpg
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