Files in cTRAP

Identification of candidate causal perturbations from differential gene expression data

NEWS.md README.md R/cTRAP-package.r R/ENCODE.R R/utils.R R/CMap.R R/plots.R R/shinyInterface.R R/drugSensitivity.R R/drugSetEnrichment.R R/cmapR_subset.R R/compare.R vignettes/cTRAP.Rmd man/getCMapPerturbationTypes.Rd man/rankColumns.Rd man/plotGSEA.Rd man/plotSingleCorr.Rd man/compareAgainstReference.Rd man/subsetToIds.Rd man/as.table.referenceComparison.Rd man/listExpressionDrugSensitivityAssociation.Rd man/predictTargetingDrugs.Rd man/GCT-class.Rd man/getCMapConditions.Rd man/findIntersectingCompounds.Rd man/chunkVector.Rd man/cmapPerturbationsKD.Rd man/calculateCellLineMean.Rd man/launchDiffExprLoader.Rd man/prepareCMapPerturbations.Rd man/counts.Rd man/plotDrugSetEnrichment.Rd man/plotMetricDistribution.Rd man/closeOpenHandles.Rd man/performGSEA.Rd man/matchStatsWithDrugSetsID.Rd man/filterCMapMetadata.Rd man/loadCTRPgeneExpression.Rd man/checkColnames.Rd man/cmapPerturbationsCompounds.Rd man/prepareDrugSets.Rd man/processByChunks.Rd man/convertENSEMBLtoGeneSymbols.Rd man/performDifferentialExpression.Rd man/cTRAP.Rd man/launchResultPlotter.Rd man/analyseDrugSetEnrichment.Rd man/readGctxIds.Rd man/dot-prepareNavPage.Rd man/plot.perturbationChanges.Rd man/getENCODEcontrols.Rd man/parseCMapID.Rd man/fix.datatypes.Rd man/processIds.Rd man/rankSimilarPerturbations.Rd man/downloadIfNotFound.Rd man/plot.referenceComparison.Rd man/launchMetadataViewer.Rd man/prepareENCODEgeneExpression.Rd man/loadENCODEsample.Rd man/performGSEAagainstReference.Rd man/loadExpressionDrugSensitivityAssociation.Rd man/loadENCODEsamples.Rd man/dot-plotBubbles.Rd man/loadCMapData.Rd man/diffExprStat.Rd man/loadCMapZscores.Rd man/plotTargetingDrugsVSsimilarPerturbations.Rd man/cmapMetadata.Rd man/stripStr.Rd man/print.similarPerturbations.Rd man/launchCMapDataLoader.Rd man/compareQuantile.Rd man/plotESplot.Rd man/downloadENCODEknockdownMetadata.Rd man/prepareExpressionDrugSensitivityAssociation.Rd man/ENCODEmetadata.Rd man/prepareGSEAgenesets.Rd man/compareAgainstReferencePerMethod.Rd man/correlateAgainstReference.Rd man/loadDrugDescriptors.Rd man/readGctxMeta.Rd man/loadNCI60drugSensitivity.Rd tests/testthat.R tests/spelling.R tests/testthat/test_CMap.R tests/testthat/test_drugSetEnrichment.R tests/testthat/test_ENCODE.R tests/testthat/test_drugSensitivity.R tests/testthat/test_plots.R inst/doc/cTRAP.R inst/doc/cTRAP.Rmd