neaGUI: A user friendly R package to perform the network enrichment analysis (NEA).

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.

Authorsetia pramana
Bioconductor views DifferentialExpression GUI Microarray
Date of publication2013-08-20 20:43:14
Maintainersetia pramana <setia.pramana@ki.se>
LicenseGPL-2
Version0.99.0

View on R-Forge

Files

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

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