analyseDrugSetEnrichment
                        Analyse drug set enrichment
as.table.referenceComparison
                        Cross Tabulation and Table Creation
cTRAP                   cTRAP package
convertENSEMBLtoGeneSymbols
                        Convert ENSEMBL gene identifiers to gene
                        symbols
downloadENCODEknockdownMetadata
                        Download metadata for ENCODE knockdown
                        experiments
filterCMapMetadata      Filter CMap metadata
getCMapConditions       List available conditions in CMap datasets
getCMapPerturbationTypes
                        Get CMap perturbation types
launchCMapDataLoader    Load CMap data via a visual interface
launchDiffExprLoader    Load differential expression data via a visual
                        interface
launchMetadataViewer    View metadata via a visual interface
launchResultPlotter     View and plot results via a visual interface
listExpressionDrugSensitivityAssociation
                        List available gene expression and drug
                        sensitivity correlation matrices
loadCMapData            Load CMap data
loadCMapZscores         Load matrix of CMap perturbation's differential
                        expression z-scores (optional)
loadDrugDescriptors     Load table with drug descriptors
loadENCODEsamples       Load ENCODE samples
loadExpressionDrugSensitivityAssociation
                        Load gene expression and drug sensitivity
                        correlation matrix
parseCMapID             Parse CMap identifier
performDifferentialExpression
                        Perform differential gene expression based on
                        ENCODE data
plot.perturbationChanges
                        Operations on a 'perturbationChanges' object
plot.referenceComparison
                        Plot data comparison
plotDrugSetEnrichment   Plot drug set enrichment
plotTargetingDrugsVSsimilarPerturbations
                        Plot similar perturbations against predicted
                        targeting drugs
predictTargetingDrugs   Predict targeting drugs
prepareCMapPerturbations
                        Prepare CMap perturbation data
prepareDrugSets         Prepare drug sets from a table with compound
                        descriptors
prepareENCODEgeneExpression
                        Load ENCODE gene expression data
print.similarPerturbations
                        Print a 'similarPerturbations' object
rankSimilarPerturbations
                        Rank CMap perturbations' similarity to a
                        differential expression profile
