# Ensemble of Gene Set Enrichment Analyses

## Documentation for package ‘EGSEA’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

EGSEA-package | Ensemble of Gene Enrichment Analysis (EGSEA)
$-method | The EGSEAResults class
$-method | The GSCollectionIndex class
buildCustomIdx | Custom Gene Set Collection Index
buildGeneSetDBIdx | Gene Set Collection Indexes from the GeneSetDB Database
buildIdx | Generate Gene Set Collection Indexes from the MSigDB and KEGG Databases
buildKEGGIdx | Gene Set Collection Index from the KEGG Database
buildMSigDBIdx | Gene Set Collection Indexes from the MSigDB Database
EGSEA | Ensemble of Gene Enrichment Analysis (EGSEA)
egsea | Ensemble of Gene Set Enrichment Analyses Function
egsea.base | EGSEA Base GSE Methods
egsea.cnt | Ensemble of Gene Set Enrichment Analyses Function
egsea.combine | EGSEA P-value Combining Options
egsea.logo | Ensemble of Gene Enrichment Analysis (EGSEA)
egsea.ora | Over-representation Analysis with EGSEA Reporting Capabilities
egsea.sort | EGSEA Result Sorting Options
EGSEAResults | The EGSEAResults class
EGSEAResults-class | The EGSEAResults class
generateReport | The EGSEAResults class
generateReport-method | The EGSEAResults class
getlimmaResults | The EGSEAResults class
getlimmaResults-method | The EGSEAResults class
getSetByID | The GSCollectionIndex class
getSetByID-method | The GSCollectionIndex class
getSetByName | The GSCollectionIndex class
getSetByName-method | The GSCollectionIndex class
getSetScores | The EGSEAResults class
getSetScores-method | The EGSEAResults class
GSCollectionIndex | The GSCollectionIndex class
GSCollectionIndex-class | The GSCollectionIndex class
limmaTopTable | The EGSEAResults class
limmaTopTable-method | The EGSEAResults class
plotBars | The EGSEAResults class
plotBars-method | The EGSEAResults class
plotGOGraph | The EGSEAResults class
plotGOGraph-method | The EGSEAResults class
plotHeatmap | The EGSEAResults class
plotHeatmap-method | The EGSEAResults class
plotMethods | The EGSEAResults class
plotMethods-method | The EGSEAResults class
plotPathway | The EGSEAResults class
plotPathway-method | The EGSEAResults class
plotSummary | The EGSEAResults class
plotSummary-method | The EGSEAResults class
plotSummaryHeatmap | The EGSEAResults class
plotSummaryHeatmap-method | The EGSEAResults class
show-method | The EGSEAResults class
show-method | The GSCollectionIndex class
showSetByID | The EGSEAResults class
showSetByID-method | The EGSEAResults class
showSetByName | The EGSEAResults class
showSetByName-method | The EGSEAResults class
summary-method | The EGSEAResults class
summary-method | The GSCollectionIndex class
topSets | The EGSEAResults class
topSets-method | The EGSEAResults class