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 |
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 for the rownames of a SummarizedExperiment |
idTypes |
Mapping between gene ID types for the rownames of a SummarizedExperiment |
isAvailable |
Is a required package available? |
makeExampleData |
Example data for the EnrichmentBrowser package |
map.ids |
Mapping between gene ID types for the rownames of a SummarizedExperiment |
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) |
spia |
Network-based enrichment analysis (NBEA) |
volcano |
Visualization of gene expression |
vst |
Variance-stabilizing transformation for RNA-seq expression data |
writeGMT |
Definition of gene sets according to different sources |