# Identification of candidate causal perturbations from differential gene expression data

## Documentation for package ‘cTRAP’ version 1.19.0

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

## Help Pages

analyseDrugSetEnrichment | Analyse drug set enrichment
as.table.referenceComparison | Cross Tabulation and Table Creation
compareAgainstCMap | Rank differential expression profile against CMap perturbations by similarity
convertENSEMBLtoGeneSymbols | Convert ENSEMBL gene identifiers to gene symbols
convertGeneIdentifiers | Convert gene identifiers
cTRAP | cTRAP package
dim.expressionDrugSensitivityAssociation | Operations on 'expressionDrugSensitivityAssociation' objects
dim.perturbationChanges | Operations on a 'perturbationChanges' object
dimnames.expressionDrugSensitivityAssociation | Operations on 'expressionDrugSensitivityAssociation' objects
dimnames.perturbationChanges | Operations on a 'perturbationChanges' object
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
launchDrugSetEnrichmentAnalyser | View and plot results 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 differential expression profile against CMap perturbations by similarity
[.expressionDrugSensitivityAssociation | Operations on 'expressionDrugSensitivityAssociation' objects
[.perturbationChanges | Operations on a 'perturbationChanges' object