Identification of candidate causal perturbations from differential gene expression data

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Documentation for package ‘cTRAP’ version 1.22.0

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

Help Pages

cTRAP-package	cTRAP package
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