Package: PharmacoGx
Type: Package
Title: Analysis of Large-Scale Pharmacogenomic Data
Version: 3.15.0
Date: 2025-05-22
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 (>= 4.1.0), 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'
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:33:56 UTC
RemoteUrl: https://github.com/bioc/PharmacoGx
RemoteRef: HEAD
RemoteSha: a1fade52bcc12a11406d00d0a5bd2ade5dd3c5f1
NeedsCompilation: yes
Packaged: 2025-11-02 15:24:37 UTC; root
Author: Petr Smirnov [aut],
  Christopher Eeles [aut],
  Jermiah Joseph [aut],
  Zhaleh Safikhani [aut],
  Mark Freeman [aut],
  Feifei Li [aut],
  Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-11-02 15:27:17 UTC; windows
Archs: x64
