DESCRIPTION

Package: PharmacoGx
Type: Package
Title: Analysis of Large-Scale Pharmacogenomic Data
Version: 3.7.5
Date: 2024-04-08
Authors@R: c(
    person(given="Petr", family="Smirnov", email="petr.smirnov@uhnresearch.ca",
        role=c("aut")),
    person(given="Christopher", family="Eeles",
        email="christopher.eeles@uhnresearch.ca", role=c("aut")),
    person(given="Jermiah", family="Joseph", 
        email="jermiah.joseph@uhn.ca", role=c("aut")),
    person(given="Zhaleh", family="Safikhani", role=c("aut")),
    person(given="Mark", family="Freeman", role=c("aut")),
    person(given="Feifei", family="Li", email="ff.li@mail.utoronto.ca", role=c("aut")),
    person("Benjamin", "Haibe-Kains", email="benjamin.haibe.kains@utoronto.ca", role=c("aut", "cre"))
    )
Description: Contains a set of functions to perform large-scale analysis of
    pharmaco-genomic data. These include the PharmacoSet object for storing
    the results of pharmacogenomic experiments, as well as a number of functions
    for computing common summaries of drug-dose response and correlating them
    with the molecular features in a cancer cell-line.
License: GPL (>= 3)
Suggests: pander,
    rmarkdown,
    knitr,
    knitcitations,
    crayon,
    testthat,
    markdown,
    BiocStyle,
    R.utils
Encoding: UTF-8
Imports:
    BiocGenerics,
    Biobase,
    S4Vectors,
    SummarizedExperiment,
    MultiAssayExperiment,
    BiocParallel,
    ggplot2,
    RColorBrewer,
    magicaxis,
    parallel,
    caTools,
    methods,
    downloader,
    stats,
    utils,
    graphics,
    grDevices,
    reshape2,
    jsonlite,
    data.table,
    checkmate,
    boot,
    coop
Depends: R (>= 3.6), CoreGx
LinkingTo: Rcpp
Roxygen: list(markdown = TRUE, r6=FALSE)
RoxygenNote: 7.3.1
VignetteBuilder: knitr
VignetteEngine: knitr::rmarkdown
biocViews: GeneExpression, Pharmacogenetics, Pharmacogenomics, Software, Classification
BugReports: https://github.com/bhklab/PharmacoGx/issues
Collate:
    'GR.R'
    'GWC.R'
    'PharmacoSet-class.R'
    'PharmacoSet-accessors.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-[.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'