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.

Author
Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Date of publication
None
Maintainer
Ludwig Geistlinger <Ludwig.Geistlinger@bio.ifi.lmu.de>
License
Artistic-2.0
Version
2.4.2

View on Bioconductor

Man pages

comb.ea.results
Combining enrichment analysis results
compile.grn.from.kegg
Compilation of a gene regulatory network from KEGG pathways
config.ebrowser
Configuring the EnrichmentBrowser
de.ana
Differential expression analysis between two sample groups
download.kegg.pathways
Download of KEGG pathways for a particular organism
ea.browse
Exploration of enrichment analysis results
ebrowser
Seamless navigation through enrichment analysis results
get.go.genesets
Definition of gene sets according to the Gene Ontology (GO)
get.kegg.genesets
Definition of gene sets according to KEGG pathways for a...
ggea.graph
GGEA graphs of consistency between regulation and expression
make.example.data
Example data for the EnrichmentBrowser package
map.ids
Mapping between gene ID types for feature names of an...
nbea
Network-based enrichment analysis (NBEA)
normalize
Normalization of microarray and RNA-seq expression data
plots
Visualization of gene expression
probe.2.gene.eset
Transformation of probe level expression to gene level...
read.eset
Reading gene expression data from file into an expression set
sbea
Set-based enrichment analysis (SBEA)

Files in this package

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