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

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Documentation for package ‘EnrichmentBrowser’ version 2.39.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

comb.ea.results	Combining enrichment analysis results
combResults	Combining enrichment analysis results
compile.grn.from.kegg	Compilation of a gene regulatory network from pathway databases
compileGRN	Compilation of a gene regulatory network from pathway databases
config.ebrowser	Configuring the EnrichmentBrowser
configEBrowser	Configuring the EnrichmentBrowser
de.ana	Differential expression analysis between two sample groups
deAna	Differential expression analysis between two sample groups
download.kegg.pathways	Download of KEGG pathways for a particular organism
downloadPathways	Download of KEGG pathways for a particular organism
ea.browse	Exploration of enrichment analysis results
eaBrowse	Exploration of enrichment analysis results
ebrowser	Seamless navigation through enrichment analysis results
export	Export results from set- and network-based enrichment analysis
exprsHeatmap	Visualization of gene expression
get.go.genesets	Definition of gene sets according to different sources
get.kegg.genesets	Definition of gene sets according to different sources
getGenesets	Definition of gene sets according to different sources
ggea	Network-based enrichment analysis (NBEA)
ggea.graph	GGEA graphs of consistency between regulation and expression
ggea.graph.legend	GGEA graphs of consistency between regulation and expression
ggeaGraph	GGEA graphs of consistency between regulation and expression
ggeaGraphLegend	GGEA graphs of consistency between regulation and expression
gs.ranking	Exploration of enrichment analysis results
gsea	Set-based enrichment analysis (SBEA)
gsRanking	Exploration of enrichment analysis results
idMap	Mapping between gene ID types
idTypes	Mapping between gene ID types
import	Import results from differential expression (DE) analysis
isAvailable	Is a required package available?
makeExampleData	Example data for the EnrichmentBrowser package
map.ids	Mapping between gene ID types
nbea	Network-based enrichment analysis (NBEA)
nbeaMethods	Network-based enrichment analysis (NBEA)
normalize	Normalization of microarray and RNA-seq expression data
ora	Set-based enrichment analysis (SBEA)
parse.genesets.from.GMT	Definition of gene sets according to different sources
pdistr	Visualization of gene expression
plots	Visualization of gene expression
probe.2.gene.eset	Transformation of probe level expression to gene level expression
probe2gene	Transformation of probe level expression to gene level expression
read.eset	Reading gene expression data from file
readSE	Reading gene expression data from file
sbea	Set-based enrichment analysis (SBEA)
sbeaMethods	Set-based enrichment analysis (SBEA)
showAvailableCollections	Definition of gene sets according to different sources
showAvailableSpecies	Definition of gene sets according to different sources
spia	Network-based enrichment analysis (NBEA)
volcano	Visualization of gene expression
writeGMT	Definition of gene sets according to different sources