EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis

The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

AuthorLudwig Geistlinger, Gergely Csaba, Ralf Zimmer
Date of publicationNone
MaintainerLudwig Geistlinger <Ludwig.Geistlinger@bio.ifi.lmu.de>
LicenseArtistic-2.0
Version2.4.6

View on Bioconductor

Functions

comb.ea.results Man page
compile.grn.from.kegg Man page
config.ebrowser Man page
de.ana Man page
download.kegg.pathways Man page
ea.browse Man page
ebrowser Man page
exprs.heatmap Man page
get.go.genesets Man page
get.kegg.genesets Man page
ggea Man page
ggea.graph Man page
ggea.graph.legend Man page
gsea Man page
gs.ranking Man page
id.types Man page
make.example.data Man page
map.ids Man page
nbea Man page
nbea.methods Man page
normalize Man page
ora Man page
parse.genesets.from.GMT Man page
pdistr Man page
probe.2.gene.eset Man page
read.eset Man page
sbea Man page
sbea.methods Man page
volcano Man page

Files

EnrichmentBrowser/DESCRIPTION
EnrichmentBrowser/NAMESPACE
EnrichmentBrowser/NEWS
EnrichmentBrowser/R
EnrichmentBrowser/R/GSEA.1.0.R EnrichmentBrowser/R/SAMGS.R EnrichmentBrowser/R/combine.R EnrichmentBrowser/R/compileGRN.R EnrichmentBrowser/R/deAna.R EnrichmentBrowser/R/downloadKEGGPathways.R EnrichmentBrowser/R/ebrowser.R EnrichmentBrowser/R/examples.R EnrichmentBrowser/R/getGenesets.R EnrichmentBrowser/R/ggea.R EnrichmentBrowser/R/ggeaGraph.R EnrichmentBrowser/R/html.R EnrichmentBrowser/R/mapIds.R EnrichmentBrowser/R/nbea.R EnrichmentBrowser/R/normalize.R EnrichmentBrowser/R/pathview2.R EnrichmentBrowser/R/plots.R EnrichmentBrowser/R/probeEset2geneEset.R EnrichmentBrowser/R/readEset.R EnrichmentBrowser/R/sbea.R EnrichmentBrowser/R/utils.R EnrichmentBrowser/R/zzz.R
EnrichmentBrowser/build
EnrichmentBrowser/build/vignette.rds
EnrichmentBrowser/inst
EnrichmentBrowser/inst/CITATION
EnrichmentBrowser/inst/doc
EnrichmentBrowser/inst/doc/EnrichmentBrowser.R
EnrichmentBrowser/inst/doc/EnrichmentBrowser.Rnw
EnrichmentBrowser/inst/doc/EnrichmentBrowser.pdf
EnrichmentBrowser/inst/extdata
EnrichmentBrowser/inst/extdata/air_lgc.tab
EnrichmentBrowser/inst/extdata/exprs.tab
EnrichmentBrowser/inst/extdata/fData.tab
EnrichmentBrowser/inst/extdata/hsa_kegg_gs.gmt
EnrichmentBrowser/inst/extdata/hsa_kegg_pwys.zip
EnrichmentBrowser/inst/extdata/pData.tab
EnrichmentBrowser/man
EnrichmentBrowser/man/comb.ea.results.Rd EnrichmentBrowser/man/compile.grn.from.kegg.Rd EnrichmentBrowser/man/config.ebrowser.Rd EnrichmentBrowser/man/de.ana.Rd EnrichmentBrowser/man/download.kegg.pathways.Rd EnrichmentBrowser/man/ea.browse.Rd EnrichmentBrowser/man/ebrowser.Rd EnrichmentBrowser/man/get.go.genesets.Rd EnrichmentBrowser/man/get.kegg.genesets.Rd EnrichmentBrowser/man/ggea.graph.Rd EnrichmentBrowser/man/make.example.data.Rd EnrichmentBrowser/man/map.ids.Rd EnrichmentBrowser/man/nbea.Rd EnrichmentBrowser/man/normalize.Rd EnrichmentBrowser/man/plots.Rd EnrichmentBrowser/man/probe.2.gene.eset.Rd EnrichmentBrowser/man/read.eset.Rd EnrichmentBrowser/man/sbea.Rd
EnrichmentBrowser/vignettes
EnrichmentBrowser/vignettes/EnrichmentBrowser.Rnw
EnrichmentBrowser/vignettes/comb_ebrowse.png
EnrichmentBrowser/vignettes/ora_ebrowse.png
EnrichmentBrowser/vignettes/refs.bib

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