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EnrichmentBrowser (version 2.2.2)

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

Description

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.

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Version

Version

2.2.2

License

Artistic-2.0

Last Published

February 15th, 2017

Functions in EnrichmentBrowser (2.2.2)

ebrowser

Seamless navigation through enrichment analysis results
get.kegg.genesets

Definition of gene sets according to KEGG pathways for a specified organism
config.ebrowser

Configuring the EnrichmentBrowser
ea.browse

Exploration of enrichment analysis results
make.example.data

Example data for the EnrichmentBrowser package
plots

Visualization of gene expression
download.kegg.pathways

Download of KEGG pathways for a particular organism
de.ana

Differential expression analysis between two sample groups
read.eset

Reading gene expression data from file into an expression set
ggea.graph

GGEA graphs of consistency between regulation and expression
normalize

Normalization of microarray and RNA-seq expression data
sbea

Set-based enrichment analysis (SBEA)
get.go.genesets

Definition of gene sets according to the Gene Ontology (GO)
compile.grn.from.kegg

Compilation of a gene regulatory network from KEGG pathways
comb.ea.results

Combining enrichment analysis results
nbea

Network-based enrichment analysis (NBEA)
probe.2.gene.eset

Transformation of probe level expression to gene level expression
map.ids

Mapping between gene ID types for feature names of an expression set