Files in nuno-agostinho/cTRAP
Identification of candidate causal perturbations from differential gene expression data
.Rbuildignore
.devcontainer/devcontainer.json
.dockerignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yaml
.github/workflows/pkgdown.yml
.github/workflows/update-license-year.yml
.gitignore
CONDUCT.md
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
NEWS.md
R/CMap.R
R/ENCODE.R
R/cTRAP-package.r
R/cmapR_subset.R
R/compare.R
R/drugSensitivity.R
R/drugSetEnrichment.R
R/floweRy.R
R/plots.R
R/shinyInterface.R
R/shinyInterface_session.R
R/sysdata.rda
R/utils.R
README.md
_pkgdown.yml
codecov.yml
data/ENCODEmetadata.rda
data/cmapMetadata.rda
data/cmapPerturbationsCompounds.rda
data/cmapPerturbationsKD.rda
data/counts.rda
data/diffExprStat.rda
dev/CMap_perturbation_cor.R
dev/CysticFibrosis.R
dev/benchmark/.gitignore
dev/benchmark/R/getEncodeDiffExpr.R
dev/benchmark/R/memoryConsumptionPlot.R
dev/benchmark/R/memoryConsumptionPlot_help.R
dev/benchmark/R/predictTargetingDrugs.R
dev/benchmark/R/rankCMapPerturbations.R
dev/benchmark/R/rankCMapPerturbations_profvis.R
dev/benchmark/README.md
dev/benchmark/scripts/convertHeaptrackToMassif.sh
dev/benchmark/scripts/predictTargetingDrugs_heaptrack.sh
dev/benchmark/scripts/runRankCMapPerturbations.sh
dev/benchmark/scripts/runRankCMapPerturbations_heaptrack.sh
dev/benchmark/scripts/runRankCMapPerturbations_profvis.sh
dev/benchmark/scripts/runRankCMapPerturbations_valgrind.sh
dev/diffExprStat.rds
dev/drugSensitivity_NCI60_HDF5.R
dev/drugSensitivity_script.R
dev/drugSensitivity_targeting_drugs_directionality.R
dev/drugSetEnrichmentAnalysis/compoundDescriptors_analysis.R
dev/drugSetEnrichmentAnalysis/compoundDescriptors_prepare.R
dev/drugSetEnrichmentAnalysis/drugSetEnrichmentAnalysis.R
dev/interface_test.R
inst/WORDLIST
inst/shiny/www/cTRAP.css
inst/shiny/www/cTRAP.js
man/ENCODEmetadata.Rd
man/GCT-class.Rd
man/HTMLfast.Rd
man/analyseDrugSetEnrichment.Rd
man/as.table.referenceComparison.Rd
man/cTRAP.Rd
man/calculateCellLineMean.Rd
man/calculateEvenlyDistributedBins.Rd
man/checkColnames.Rd
man/chunkColumns.Rd
man/closeOpenHandles.Rd
man/cmapMetadata.Rd
man/cmapPerturbationsCompounds.Rd
man/cmapPerturbationsKD.Rd
man/compareQuantile.Rd
man/compareWithAllMethods.Rd
man/convertENSEMBLtoGeneSymbols.Rd
man/convertGeneIdentifiers.Rd
man/counts.Rd
man/diffExprStat.Rd
man/dimnames.expressionDrugSensitivityAssociation.Rd
man/dot-plotBubbles.Rd
man/dot-prepareNavPage.Rd
man/dot-traceInList.Rd
man/downloadENCODEknockdownMetadata.Rd
man/downloadIfNotFound.Rd
man/filterCMapMetadata.Rd
man/findIntersectingCompounds.Rd
man/fix.datatypes.Rd
man/getCMapConditions.Rd
man/getCMapPerturbationTypes.Rd
man/getENCODEcontrols.Rd
man/launchCMapDataLoader.Rd
man/launchDiffExprLoader.Rd
man/launchDrugSetEnrichmentAnalyser.Rd
man/launchMetadataViewer.Rd
man/launchResultPlotter.Rd
man/listExpressionDrugSensitivityAssociation.Rd
man/loadCMapData.Rd
man/loadCMapZscores.Rd
man/loadCTRPgeneExpression.Rd
man/loadDrugDescriptors.Rd
man/loadENCODEsample.Rd
man/loadENCODEsamples.Rd
man/loadExpressionDrugSensitivityAssociation.Rd
man/loadNCI60drugSensitivity.Rd
man/matchStatsWithDrugSetsID.Rd
man/parseCMapID.Rd
man/performDifferentialExpression.Rd
man/performGSEA.Rd
man/plot.perturbationChanges.Rd
man/plot.referenceComparison.Rd
man/plotDrugSetEnrichment.Rd
man/plotESplot.Rd
man/plotGSEA.Rd
man/plotMetricDistribution.Rd
man/plotSingleCorr.Rd
man/plotTargetingDrugsVSsimilarPerturbations.Rd
man/predictTargetingDrugs.Rd
man/prepareCMapPerturbations.Rd
man/prepareDrugSets.Rd
man/prepareENCODEgeneExpression.Rd
man/prepareExpressionDrugSensitivityAssociation.Rd
man/prepareGSEAgenesets.Rd
man/prepareSetsCompoundInfo.Rd
man/prepareStatsCompoundInfo.Rd
man/prepareWordBreak.Rd
man/print.similarPerturbations.Rd
man/processByChunks.Rd
man/processIds.Rd
man/rankAgainstReference.Rd
man/rankColumns.Rd
man/rankSimilarPerturbations.Rd
man/readGctxIds.Rd
man/readGctxMeta.Rd
man/stripStr.Rd
man/subsetData.Rd
man/subsetDim.Rd
man/subsetToIds.Rd
tests/spelling.R
tests/testthat.R
tests/testthat/test_CMap.R
tests/testthat/test_ENCODE.R
tests/testthat/test_drugSensitivity.R
tests/testthat/test_drugSetEnrichment.R
tests/testthat/test_plots.R
vignettes/cTRAP.Rmd
