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

## Documentation for package ‘EnrichmentBrowser’ version 2.40.0

- 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