Interactive functions

launchDiffExprLoader()

Load differential expression data via a visual interface

launchCMapDataLoader()

Load CMap data via a visual interface

launchResultPlotter()

View and plot results via a visual interface

launchMetadataViewer()

View metadata via a visual interface

launchDrugSetEnrichmentAnalyser()

View and plot results via a visual interface

Prepare ENCODE data

downloadENCODEknockdownMetadata()

Download metadata for ENCODE knockdown experiments

loadENCODEsamples()

Load ENCODE samples

prepareENCODEgeneExpression()

Load ENCODE gene expression data

convertGeneIdentifiers()

Convert gene identifiers

performDifferentialExpression()

Perform differential gene expression based on ENCODE data

Download and manipulate CMap perturbation data

getCMapConditions()

List available conditions in CMap datasets

getCMapPerturbationTypes()

Get CMap perturbation types

loadCMapData()

Load CMap data

loadCMapZscores()

Load matrix of CMap perturbation's differential expression z-scores (optional)

filterCMapMetadata()

Filter CMap metadata

prepareCMapPerturbations()

Prepare CMap perturbation data

plot(<perturbationChanges>) `[`(<perturbationChanges>) dim(<perturbationChanges>) dimnames(<perturbationChanges>)

Operations on a perturbationChanges object

parseCMapID()

Parse CMap identifier

Rank similar CMap perturbations

rankSimilarPerturbations()

Rank differential expression profile against CMap perturbations by similarity

plot(<referenceComparison>)

Plot data comparison

as.table(<referenceComparison>)

Cross Tabulation and Table Creation

plotTargetingDrugsVSsimilarPerturbations()

Plot similar perturbations against predicted targeting drugs

Predict targeting drugs

listExpressionDrugSensitivityAssociation()

List available gene expression and drug sensitivity correlation matrices

loadExpressionDrugSensitivityAssociation()

Load gene expression and drug sensitivity correlation matrix

predictTargetingDrugs()

Predict targeting drugs

plot(<referenceComparison>)

Plot data comparison

as.table(<referenceComparison>)

Cross Tabulation and Table Creation

plotTargetingDrugsVSsimilarPerturbations()

Plot similar perturbations against predicted targeting drugs

Analyse drug (descriptor) set enrichment

loadDrugDescriptors()

Load table with drug descriptors

prepareDrugSets()

Prepare drug sets from a table with compound descriptors

analyseDrugSetEnrichment()

Analyse drug set enrichment

plotDrugSetEnrichment()

Plot drug set enrichment