Files in bhklab/PharmacoGx
Analysis of Large-Scale Pharmacogenomic Data
.Rbuildignore
.Rinstignore
.gitattributes
.github/.gitignore
.github/ISSUE_TEMPLATE/bug-report--question-or-feature-request.md
.github/workflows/R-CMD-check-bioc-release.yml
.github/workflows/R-CMD-check-bioc.yml
.github/workflows/pkgdown.yaml
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/GR.R
R/GWC.R
R/PharmacoSet-accessors.R
R/PharmacoSet-class.R
R/PharmacoSet-utils.R
R/RcppExports.R
R/adaptiveMatthewCor.R
R/callingWaterfall.R
R/class-SignatureClass.R
R/computeABC.R
R/computeAUC.R
R/computeAUC_old.R
R/computeAmax.R
R/computeDSS.R
R/computeDrugSensitivity.R
R/computeGR.R
R/computeIC50.R
R/computeICn.R
R/computeSlope.R
R/computeSynergy.R
R/connectivityScore.R
R/cosinePerm.R
R/datasets.R
R/downloadPSet.R
R/downloadSignatures.R
R/drugDoseResponseCurve.R
R/drugPerturbationSig.R
R/filterNoisyCurves.R
R/geneDrugPerturbation.R
R/geneDrugSensitivity.R
R/geneDrugSensitivityPBCorr.R
R/geneDrugSensitivityPCorr.R
R/getRawSensitivityMatrix.R
R/globals.R
R/intersectPSets.R
R/logLogisticRegression.R
R/matthewCor.R
R/mergePSets.R
R/methods-[.R
R/methods-drugSensitivitySig.R
R/methods-intersect.R
R/methods-subsetTo.R
R/methods-summarizeMolecularProfiles.R
R/methods-summarizeSensitivityProfiles.R
R/plotPSig.R
R/rankGeneDrugPerturbation.R
R/rankGeneDrugSensitivity.R
R/sanityCheck.R
R/updateObject-methods.R
R/zzz.R
README.md
_pkgdown.yml
codecover.R
data/CCLEsmall.rda
data/CMAPsmall.rda
data/GDSCsmall.rda
data/HDAC_genes.rda
inst/CITATION
inst/PharmacoGx_Molecular_Data_Standards.md
inst/extdata/mathews_griner.csv.tar.gz
man/CCLEsmall.Rd
man/CMAPsmall.Rd
man/GDSCsmall.Rd
man/HDAC_genes.Rd
man/PharmacoSet-accessors.Rd
man/PharmacoSet-class.Rd
man/PharmacoSet-utils.Rd
man/PharmacoSet.Rd
man/PharmacoSet2.Rd
man/PharmacoSig.Rd
man/amcc.Rd
man/availablePSets.Rd
man/callingWaterfall.Rd
man/checkPsetStructure.Rd
man/computeABC.Rd
man/computeAUC.Rd
man/computeAmax.Rd
man/computeBliss.Rd
man/computeHSA.Rd
man/computeICn.Rd
man/computeLoewe.Rd
man/computeSlope.Rd
man/computeZIP.Rd
man/computeZIPdelta-TreatmentResponseExperiment-method.Rd
man/computeZIPdelta.Rd
man/connectivityScore.Rd
man/cosinePerm.Rd
man/dim-PharmacoSet-method.Rd
man/dot-computeZIPdelta.Rd
man/dot-summarizeSensProfiles.Rd
man/downloadPSet.Rd
man/downloadPertSig.Rd
man/drugDoseResponseCurve.Rd
man/drugPerturbationSig.Rd
man/drugSensitivitySig-PharmacoSet-method.Rd
man/effectToDose.Rd
man/estimateProjParams.Rd
man/filterNoisyCurves.Rd
man/fitTwowayZIP.Rd
man/geneDrugSensitivity.Rd
man/geneDrugSensitivityPBCorr.Rd
man/geneDrugSensitivityPCorr.Rd
man/gwc.Rd
man/hillCurve.Rd
man/intersectPSet.Rd
man/loeweCI.Rd
man/logLogisticRegression.Rd
man/mcc.Rd
man/partialCorQUICKSTOP.Rd
man/plot.PharmacoSig.Rd
man/show-PharmacoSet-method.Rd
man/show-PharmacoSig-method.Rd
man/showSigAnnot-PharmacoSig-method.Rd
man/sub-PharmacoSet-ANY-ANY-ANY-method.Rd
man/subsetTo-PharmacoSet-method.Rd
man/summarizeMolecularProfiles-PharmacoSet-method.Rd
man/summarizeSensitivityProfiles-PharmacoSet-method.Rd
man/updateObject-PharmacoSet-method.Rd
src/RcppExports.cpp
src/metaPermC.c
src/rCPP_bridge.cpp
tests/testthat.R
tests/testthat/cellInfo.GDSCsmall.rds
tests/testthat/cellNames.GDSCsmall.rds
tests/testthat/drug.perturbationSmall.rds
tests/testthat/drug.sensitivity.MANOVAGDSCSmall.rds
tests/testthat/drug.sensitivity.discreteGDSCSmall.rds
tests/testthat/drug.sensitivityGDSCSmall.rds
tests/testthat/drugInfo.GDSCsmall.rds
tests/testthat/drugNames.GDSCsmall.rds
tests/testthat/fNames.GDSCsmall.rds
tests/testthat/featureInfo.GDSCsmall.rds
tests/testthat/intersectedSmallData.rds
tests/testthat/intersectedSmallDataStrict.rds
tests/testthat/molecularProfiles.GDSCsmall.rds
tests/testthat/phenoInfo.GDSCsmall.rds
tests/testthat/sensitivityInfo.GDSCsmall.rds
tests/testthat/sensitivityMeasures.GDSCsmall.rds
tests/testthat/sensitivityProfiles.GDSCsmall.rds
tests/testthat/subsetTo.CMAPsmaller.rds
tests/testthat/test_Hill.R
tests/testthat/test_PharmacoSetClass.R
tests/testthat/test_PharmacoSet_utils.R
tests/testthat/test_computeABC.R
tests/testthat/test_computeIC50.R
tests/testthat/test_drugPerturbationSig.R
tests/testthat/test_drugSensitivitySig.R
tests/testthat/test_intersectPSet.R
tests/testthat/test_logLogisticRegression.R
tests/testthat/test_sanitizeInput.R
tests/testthat/test_subsetTo.R
tests/testthat/test_summarizeMolecularProfiles.R
tests/testthat/test_summarizeSensitivityProfiles.R
tests/testthat/test_unionList.R
vignettes/CreatingPharmacoSet.Rmd
vignettes/DetectingDrugSynergyAndAntagonism.R
vignettes/DetectingDrugSynergyAndAntagonism.Rmd
vignettes/PharmacoGx.Rmd
vignettes/drugCombos.bib
vignettes/pharmacogx.bib
