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>|
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)