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

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Documentation for package ‘EnrichmentBrowser’ version 2.22.2

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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