├── .Rbuildignore ├── .Rinstignore ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ └── bug-report--question-or-feature-request.md └── workflows │ ├── R-CMD-check-bioc-release.yml.deprecated │ ├── R-CMD-check-bioc.yml.deprecated │ ├── check-bioc.yml │ └── pkgdown.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── Dockerfile ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── GR.R ├── GWC.R ├── PharmacoSet-accessors.R ├── PharmacoSet-class.R ├── PharmacoSet-utils.R ├── RcppExports.R ├── adaptiveMatthewCor.R ├── callingWaterfall.R ├── class-SignatureClass.R ├── computeABC.R ├── computeAUC.R ├── computeAUC_old.R ├── computeAmax.R ├── computeDSS.R ├── computeDrugSensitivity.R ├── computeGR.R ├── computeIC50.R ├── computeICn.R ├── computeSlope.R ├── computeSynergy.R ├── connectivityScore.R ├── cosinePerm.R ├── datasets.R ├── downloadPSet.R ├── downloadSignatures.R ├── drugDoseResponseCurve.R ├── drugPerturbationSig.R ├── filterNoisyCurves.R ├── geneDrugPerturbation.R ├── geneDrugSensitivity.R ├── geneDrugSensitivityPBCorr.R ├── geneDrugSensitivityPCorr.R ├── getRawSensitivityMatrix.R ├── globals.R ├── intersectPSets.R ├── logLogisticRegression.R ├── matthewCor.R ├── mergePSets.R ├── methods-View.R ├── methods-[.R ├── methods-drugSensitivitySig.R ├── methods-intersect.R ├── methods-subsetTo.R ├── methods-summarizeMolecularProfiles.R ├── methods-summarizeSensitivityProfiles.R ├── plotPSig.R ├── rankGeneDrugPerturbation.R ├── rankGeneDrugSensitivity.R ├── sanityCheck.R ├── updateObject-methods.R └── zzz.R ├── README.md ├── _pkgdown.yml ├── codecover.R ├── data ├── CCLEsmall.rda ├── CMAPsmall.rda ├── GDSCsmall.rda └── HDAC_genes.rda ├── inst ├── CITATION ├── PharmacoGx_Molecular_Data_Standards.md └── extdata │ └── mathews_griner.csv.tar.gz ├── man ├── CCLEsmall.Rd ├── CMAPsmall.Rd ├── GDSCsmall.Rd ├── HDAC_genes.Rd ├── PharmacoSet-accessors.Rd ├── PharmacoSet-class.Rd ├── PharmacoSet-utils.Rd ├── PharmacoSet.Rd ├── PharmacoSet2.Rd ├── PharmacoSig.Rd ├── View.Rd ├── amcc.Rd ├── availablePSets.Rd ├── callingWaterfall.Rd ├── checkPsetStructure.Rd ├── computeABC.Rd ├── computeAUC.Rd ├── computeAmax.Rd ├── computeBliss.Rd ├── computeHSA.Rd ├── computeICn.Rd ├── computeLoewe.Rd ├── computeSlope.Rd ├── computeZIP.Rd ├── computeZIPdelta-TreatmentResponseExperiment-method.Rd ├── computeZIPdelta.Rd ├── connectivityScore.Rd ├── cosinePerm.Rd ├── dim-PharmacoSet-method.Rd ├── dot-computeZIPdelta.Rd ├── dot-summarizeSensProfiles.Rd ├── downloadPSet.Rd ├── downloadPertSig.Rd ├── drugDoseResponseCurve.Rd ├── drugPerturbationSig.Rd ├── drugSensitivitySig-PharmacoSet-method.Rd ├── effectToDose.Rd ├── estimateProjParams.Rd ├── filterNoisyCurves.Rd ├── fitTwowayZIP.Rd ├── geneDrugSensitivity.Rd ├── geneDrugSensitivityPBCorr.Rd ├── geneDrugSensitivityPCorr.Rd ├── gwc.Rd ├── hillCurve.Rd ├── intersectPSet.Rd ├── loeweCI.Rd ├── logLogisticRegression.Rd ├── mcc.Rd ├── partialCorQUICKSTOP.Rd ├── plot.PharmacoSig.Rd ├── show-PharmacoSet-method.Rd ├── show-PharmacoSig-method.Rd ├── showSigAnnot-PharmacoSig-method.Rd ├── sub-PharmacoSet-ANY-ANY-ANY-method.Rd ├── subsetTo-PharmacoSet-method.Rd ├── summarizeMolecularProfiles-PharmacoSet-method.Rd ├── summarizeSensitivityProfiles-PharmacoSet-method.Rd └── updateObject-PharmacoSet-method.Rd ├── src ├── RcppExports.cpp ├── metaPermC.c └── rCPP_bridge.cpp ├── tests ├── testthat.R └── testthat │ ├── cellInfo.GDSCsmall.rds │ ├── cellNames.GDSCsmall.rds │ ├── drug.perturbationSmall.rds │ ├── drug.sensitivity.MANOVAGDSCSmall.rds │ ├── drug.sensitivity.discreteGDSCSmall.rds │ ├── drug.sensitivityGDSCSmall.rds │ ├── drugInfo.GDSCsmall.rds │ ├── drugNames.GDSCsmall.rds │ ├── fNames.GDSCsmall.rds │ ├── featureInfo.GDSCsmall.rds │ ├── intersectedSmallData.rds │ ├── intersectedSmallDataStrict.rds │ ├── molecularProfiles.GDSCsmall.rds │ ├── phenoInfo.GDSCsmall.rds │ ├── sensitivityInfo.GDSCsmall.rds │ ├── sensitivityMeasures.GDSCsmall.rds │ ├── 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