SummarizedExperiment, S4Vectors, Biobase, parallel,
BiocParallel, RColorBrewer, caTools, magicaxis, methods,
reshape2, scales, grDevices, graphics, stats, utils,
assertthat, matrixStats, downloader

Software, Pharmacogenetics, QualityControl, Survival,
Pharmacogenomics, Classification

Venkata Manem [aut],
  Petr Smirnov [aut],
  Ian Smith [aut],
  Meghan Lambie [aut],
  Christopher Eeles [aut],
  Scott Bratman [aut],
  Benjamin Haibe-Kains [aut, cre]

Analysis of Large-Scale Pharmacogenomic Data

c(
  person("Petr", "Smirnov", email="petr.smirnov@uhnresearch.ca", role=c("aut")),
  person("Zhaleh", "Safikhani", role=c("aut")),
  person("Christopher", "Eeles", email="christopher.eeles@uhnresearch.ca", role=c("aut")),
  person("Mark", "Freeman", role=c("aut")),
  person("Benjamin", "Haibe-Kains", email="benjamin.haibe.kains@utoronto.ca", role=c("aut", "cre"))
  )

Contains a set of functions to perform large-scale analysis of pharmaco-genomic data.

Biobase, S4Vectors, SummarizedExperiment, BiocParallel,
ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods,
downloader, stats, utils, graphics, grDevices, reshape2,
testthat, jsonlite

'AdaptiveMatthewCor.R' 'ComputeGR.R' 'GR.R' 'GWC.R'
'LogLogisticRegression.R' 'MatthewCor.R' 'SanityCheck.R'
'callingWaterfall.R' 'class-PharmacoSet.R'
'class-SignatureClass.R' 'computeABC.R' 'computeAUC.R'
'computeAUC_old.R' 'computeAmax.R' 'computeDSS.R'
'computeDrugSensitivity.R' 'computeIC50.R' 'computeICn.R'
'computeSlope.R' 'connectivityScore.R' 'cosinePerm.R'
'datasets.R' 'downloadPSet.R' 'downloadSignatures.R'
'drugDoseResponseCurve.R' 'drugPerturbationSig.R'
'filterNoisyCurves.R' 'geneDrugPerturbation.R'
'geneDrugSensitivity.R' 'generics.R'
'getRawSensitivityMatrix.R' 'globals.R' 'intersectPSets.R'
'methods-cellInfo.R' 'methods-cellNames.R'
'methods-dateCreated.R' 'methods-drugInfo.R'
'methods-drugNames.R' 'methods-drugSensitivitySig.R'
'methods-fNames.R' 'methods-featureInfo.R'
'methods-mDataNames.R' 'methods-molecularProfiles.R'
'methods-molecularProfilesSlot.R' 'methods-name.R'
'methods-pertNumber.R' 'methods-phenoInfo.R'
'methods-sensNumber.R' 'methods-sensitivityInfo.R'
'methods-sensitivityMeasures.R' 'methods-sensitivityProfiles.R'
'methods-sensitivityRaw.R' 'methods-sensitivitySlot.R'
'methods-subsetTo.R' 'methods-summarizeMolecularProfiles.R'
'methods-summarizeSensitivityProfiles.R' 'plotPSig.R'
'rankGeneDrugPerturbation.R' 'rankGeneDrugSensitivity.R'
'utilities.R'