EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis
Version 2.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorLudwig Geistlinger, Gergely Csaba, Ralf Zimmer
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment GraphAndNetwork Microarray Network NetworkEnrichment Pathways RNASeq ReportWriting Visualization
Date of publicationNone
MaintainerLudwig Geistlinger <Ludwig.Geistlinger@bio.ifi.lmu.de>
LicenseArtistic-2.0
Version2.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EnrichmentBrowser")

Man pages

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)

Functions

GS.format.dataframe.to.list Source code
GSEA Source code
GSEA.EnrichmentScore Source code
GSEA.EnrichmentScore2 Source code
GSEA.GeneRanking Source code
SAMGS Source code
anno.p2g Source code
anno.pkg.2.org Source code
approx.pval Source code
auto.create.gsets Source code
auto.detect.data.type Source code
auto.detect.gs.type Source code
autoDetectGeneIdType Source code
availableOrgPkgs Source code
cepa Source code
clipper Source code
comb.ea.results Man page Source code
comb.ranks Source code
comp.de Source code
compile.grn.from.kegg Man page Source code
config.ebrowser Man page Source code
construct.ggea.graph Source code
create.index Source code
de.ana Man page Source code
degraph Source code
determine.edge.color Source code
determine.edge.lwd Source code
determine.node.color Source code
download.kegg.genesets Source code
download.kegg.pathways Man page Source code
ea.browse Man page Source code
ebm Source code
ebrowser Man page Source code
exprs.heatmap Man page Source code
extr.pwy.dat Source code
extract.kegg.genesets Source code
extract.pwys Source code
fisher.comb Source code
ganpa Source code
gene.report Source code
gene.table Source code
get.edge.type Source code
get.gene.annotation Source code
get.gene.freq.weights Source code
get.genes.by.pathway Source code
get.go.genesets Man page Source code
get.html.of.marked.pathway Source code
get.kegg.display.name Source code
get.kegg.genesets Man page Source code
get.kegg.rels.of.organism Source code
get.node.name Source code
get.ranks Source code
getOrgIdType Source code
ggea Man page Source code
ggea.graph Man page Source code
ggea.graph.legend Man page Source code
global.GSA Source code
global.GSEA Source code
global.PADOG Source code
global.SAMGS Source code
globaltest Source code
gmt2cmat Source code
grn2adjm Source code
grn2gnet Source code
gs.list.2.gs.coll Source code
gs.ranking Man page Source code
gsa Source code
gsea Man page Source code
gsva Source code
id.types Man page Source code
is.consistent Source code
is.sig Source code
is.wholenumber Source code
local.de.ana Source code
local.s2n Source code
local.t.SAM Source code
make.example.data Man page Source code
make.exmpl.ea.res Source code
make.exmpl.eset Source code
make.exmpl.grn Source code
make.exmpl.gs Source code
make.ggraph.html Source code
make.gs.names Source code
make.hmap.html Source code
make.kgraph.html Source code
make.kpath.html Source code
make.spia.data Source code
make.view Source code
make.volc.html Source code
map.ids Man page Source code
mgsa Source code
na.treat Source code
nbea Man page Source code
nbea.methods Man page Source code
ncbi.gene.link Source code
nea Source code
netgsa Source code
normalize Man page Source code
onLoad Source code
ora Man page Source code
ora.hyperg Source code
org2pkg Source code
padog Source code
parse.genesets.from.GMT Man page Source code
pathnet Source code
pathview2 Source code
pdistr Man page Source code
perm.edges.pval Source code
perm.genes.pval Source code
perm.samples.pval Source code
plot.ggea.graph Source code
prep.gsets Source code
probe.2.gene.eset Man page Source code
pruneGRN Source code
pubmed.link Source code
query.grn Source code
read.eset Man page Source code
read.grn Source code
roast.camera Source code
rowMeansVars Source code
rseq.sbea Source code
sAvailable Source code
sam.TlikeStat Source code
sbea Man page Source code
sbea.methods Man page Source code
score.grn Source code
set.out.dir Source code
spia Source code
stouffer.comb Source code
topogsa Source code
transform.grn Source code
transform.gs Source code
view.graph Source code
view.path Source code
view.set Source code
volcano Man page Source code
write.gmt Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GSEA.1.0.R
R/SAMGS.R
R/combine.R
R/compileGRN.R
R/deAna.R
R/downloadKEGGPathways.R
R/ebrowser.R
R/examples.R
R/getGenesets.R
R/ggea.R
R/ggeaGraph.R
R/html.R
R/mapIds.R
R/nbea.R
R/normalize.R
R/pathview2.R
R/plots.R
R/probeEset2geneEset.R
R/readEset.R
R/sbea.R
R/utils.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/EnrichmentBrowser.R
inst/doc/EnrichmentBrowser.Rnw
inst/doc/EnrichmentBrowser.pdf
inst/extdata
inst/extdata/air_lgc.tab
inst/extdata/exprs.tab
inst/extdata/fData.tab
inst/extdata/hsa_kegg_gs.gmt
inst/extdata/hsa_kegg_pwys.zip
inst/extdata/pData.tab
man
man/comb.ea.results.Rd
man/compile.grn.from.kegg.Rd
man/config.ebrowser.Rd
man/de.ana.Rd
man/download.kegg.pathways.Rd
man/ea.browse.Rd
man/ebrowser.Rd
man/get.go.genesets.Rd
man/get.kegg.genesets.Rd
man/ggea.graph.Rd
man/make.example.data.Rd
man/map.ids.Rd
man/nbea.Rd
man/normalize.Rd
man/plots.Rd
man/probe.2.gene.eset.Rd
man/read.eset.Rd
man/sbea.Rd
vignettes
vignettes/EnrichmentBrowser.Rnw
vignettes/comb_ebrowse.png
vignettes/ora_ebrowse.png
vignettes/refs.bib
EnrichmentBrowser documentation built on May 20, 2017, 10:36 p.m.