[.perturbationChanges   Subset a 'perturbationChanges' object
analyseDrugSetEnrichment
                        Analyse drug set enrichment
as.table.similarPerturbations
                        Cross Tabulation and Table Creation
cTRAP                   cTRAP package
compareAgainstReference
                        Compare multiple methods and rank reference
                        accordingly
convertENSEMBLtoGeneSymbols
                        Convert ENSEMBL gene identifiers to gene
                        symbols
dim.perturbationChanges
                        Dimensions of a 'perturbationChanges' object
dimnames.perturbationChanges
                        Dimnames of a 'perturbationChanges' object
downloadENCODEknockdownMetadata
                        Download metadata for ENCODE knockdown
                        experiments
filterCMapMetadata      Filter CMap metadata
getCMapConditions       List available conditions in CMap datasets
getCMapPerturbationTypes
                        Get perturbation types
loadCMapData            Load CMap data
loadCMapZscores         Load matrix of CMap perturbation's differential
                        expression z-scores
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
                        Plot perturbation comparison against a
                        differential expression profile
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 an ENCODE gene expression data
print.similarPerturbations
                        Print a 'similarPerturbations' object
rankSimilarPerturbations
                        Rank CMap perturbations' similarity to a
                        differential expression profile
