Identification of candidate causal perturbations from differential gene expression data

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Documentation for package ‘cTRAP’ version 1.6.0

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cTRAP-package cTRAP package
analyseDrugSetEnrichment Analyse drug set enrichment
as.table.similarPerturbations Cross Tabulation and Table Creation
compareAgainstCMap Rank CMap perturbations' similarity to a differential expression profile
compareAgainstReference Compare multiple methods and rank reference accordingly
convertENSEMBLtoGeneSymbols Convert ENSEMBL gene identifiers to gene symbols
cTRAP cTRAP package
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
[.perturbationChanges Subset a 'perturbationChanges' object