# Ensemble of Gene Set Enrichment Analyses

## Documentation for package ‘EGSEA’ version 1.6.1

- 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 | Functions to create gene set collection indexes for EGSEA
buildCustomIdx,egsea-index | Functions to create gene set collection indexes for EGSEA
buildGeneSetDBIdx | Functions to create gene set collection indexes for EGSEA
buildGeneSetDBIdx,egsea-index | Functions to create gene set collection indexes for EGSEA
buildGMTIdx | Functions to create gene set collection indexes for EGSEA
buildGMTIdx,egsea-index | Functions to create gene set collection indexes for EGSEA
buildIdx | Functions to create gene set collection indexes for EGSEA
buildIdx,egsea-index | Functions to create gene set collection indexes for EGSEA
buildKEGGIdx | Functions to create gene set collection indexes for EGSEA
buildKEGGIdx,egsea-index | Functions to create gene set collection indexes for EGSEA
buildMSigDBIdx | Functions to create gene set collection indexes for EGSEA
buildMSigDBIdx,egsea-index | Functions to create gene set collection indexes for EGSEA
EGSEA | Ensemble of Gene Enrichment Analysis (EGSEA)
egsea | Core functions to perform ensemble of gene set enrichment analysis (EGSEA)
egsea,egsea-main | Core functions to perform ensemble of gene set enrichment analysis (EGSEA)
egsea.base | EGSEA auxiliary functions
egsea.base,egsea-aux | EGSEA auxiliary functions
egsea.cnt | Core functions to perform ensemble of gene set enrichment analysis (EGSEA)
egsea.cnt,egsea-main | Core functions to perform ensemble of gene set enrichment analysis (EGSEA)
egsea.combine | EGSEA auxiliary functions
egsea.combine,egsea-aux | EGSEA auxiliary functions
egsea.logo | EGSEA auxiliary functions
egsea.logo,egsea-aux | EGSEA auxiliary functions
egsea.ma | Core functions to perform ensemble of gene set enrichment analysis (EGSEA)
egsea.ora | Core functions to perform ensemble of gene set enrichment analysis (EGSEA)
egsea.ora,egsea-main | Core functions to perform ensemble of gene set enrichment analysis (EGSEA)
egsea.sort | EGSEA auxiliary functions
egsea.sort,egsea-aux | EGSEA auxiliary functions
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