API for nuno-agostinho/cTRAP
Identification of candidate causal perturbations from differential gene expression data

Global functions
ENCODEmetadata Man page
GCT-class Man page
[.perturbationChanges Man page
`[.perturbationChanges` Source code
analyseDrugSetEnrichment Man page Source code
as.table.similarPerturbations Man page Source code
cTRAP Man page
cTRAP-package Man page
calculateCellLineMean Man page Source code
checkColnames Man page Source code
chunkVector Man page Source code
closeOpenHandles Man page Source code
cmapMetadata Man page
cmapPerturbationsCompounds Man page
cmapPerturbationsKD Man page
compareAgainstCMap Man page
compareAgainstReference Man page Source code
compareAgainstReferencePerMethod Man page Source code
compareQuantile Man page Source code
convertENSEMBLtoGeneSymbols Man page Source code
correlateAgainstReference Man page Source code
correlateGEandDrugSensitivity Source code
counts Man page
diffExprStat Man page
dim.perturbationChanges Man page Source code
dimnames.perturbationChanges Man page Source code
downloadENCODEknockdownMetadata Man page Source code
downloadIfNotFound Man page Source code
filterCMapMetadata Man page Source code
fix.datatypes Man page Source code
getCMapConditions Man page Source code
getCMapPerturbationTypes Man page
getENCODEcontrols Man page Source code
loadCMapCompoundInfo Source code
loadCMapData Man page Source code
loadCMapGeneInfo Source code
loadCMapMetadata Source code
loadCMapZscores Man page Source code
loadCTRPcompoundInfo Man page Source code
loadCTRPdrugSensitivity Man page Source code
loadCTRPgeneExpression Man page Source code
loadDrugDescriptors Man page Source code
loadENCODEsample Man page
loadENCODEsamples Man page Source code
loadExpressionDrugSensitivityAssociation Man page Source code
loadGDSC7cellLineInfo Man page Source code
loadGDSC7compoundInfo Man page Source code
loadGDSC7drugSensitivity Man page Source code
loadGDSC7file Man page Source code
loadGDSC7geneExpression Man page Source code
loadNCI60drugSensitivity Man page Source code
loadNCI60geneExpression Man page Source code
matchStatsWithDrugSetsID Man page Source code
parseCMapID Man page Source code
performDifferentialExpression Man page Source code
performGSEA Man page Source code
performGSEAagainstReference Man page Source code
plot.perturbationChanges Man page Source code
plot.referenceComparison Man page Source code
plotDrugSetEnrichment Man page Source code
plotESplot Man page Source code
plotGSEA Man page Source code
plotMetricDistribution Man page Source code
plotSingleCorr Man page Source code
plotTargetingDrugsVSsimilarPerturbations Man page Source code
predictTargetingDrugs Man page Source code
prepareCMapPerturbations Man page Source code
prepareCMapZscores Source code
prepareDrugSets Man page Source code
prepareENCODEgeneExpression Man page Source code
prepareExpressionDrugSensitivityAssociation Man page Source code
prepareGSEApathways Man page Source code
prepareLabel Source code
print.similarPerturbations Man page Source code
processByChunks Man page Source code
processCall Source code
processChunk Source code
processIds Man page Source code
processStats Source code
rankColumns Man page Source code
rankSimilarPerturbations Man page Source code
readGctxIds Man page Source code
readGctxMeta Man page Source code
stripStr Man page Source code
subsetToIds Man page Source code
nuno-agostinho/cTRAP documentation built on Nov. 13, 2019, 3:31 p.m.