{
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  "Package": "PharmacoGx",
  "Type": "Package",
  "Title": "Analysis of Large-Scale Pharmacogenomic Data",
  "Version": "3.17.0",
  "Date": "2025-05-22",
  "Authors@R": "c(\nperson(given=\"Petr\", family=\"Smirnov\", email=\"petr.smirnov@uhnresearch.ca\",\nrole=c(\"aut\")),\nperson(given=\"Christopher\", family=\"Eeles\",\nemail=\"christopher.eeles@uhnresearch.ca\", role=c(\"aut\")),\nperson(given=\"Jermiah\", family=\"Joseph\",\nemail=\"jermiah.joseph@uhn.ca\", role=c(\"aut\")),\nperson(given=\"Zhaleh\", family=\"Safikhani\", role=c(\"aut\")),\nperson(given=\"Mark\", family=\"Freeman\", role=c(\"aut\")),\nperson(given=\"Feifei\", family=\"Li\", email=\"ff.li@mail.utoronto.ca\", role=c(\"aut\")),\nperson(\"Benjamin\", \"Haibe-Kains\", email=\"benjamin.haibe.kains@utoronto.ca\", role=c(\"aut\", \"cre\"))\n)",
  "Description": "Contains a set of functions to perform large-scale\nanalysis of pharmaco-genomic data. These include the\nPharmacoSet object for storing the results of pharmacogenomic\nexperiments, as well as a number of functions for computing\ncommon summaries of drug-dose response and correlating them\nwith the molecular features in a cancer cell-line.",
  "License": "GPL (>= 3)",
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  "biocViews": "GeneExpression, Pharmacogenetics, Pharmacogenomics,\nSoftware, Classification",
  "BugReports": "https://github.com/bhklab/PharmacoGx/issues",
  "Collate": "'GR.R' 'GWC.R' 'PharmacoSet-class.R' 'PharmacoSet-accessors.R'\n'PharmacoSet-utils.R' 'RcppExports.R' 'adaptiveMatthewCor.R'\n'callingWaterfall.R' 'class-SignatureClass.R' 'computeABC.R'\n'computeAUC.R' 'computeAUC_old.R' 'computeAmax.R'\n'computeDSS.R' 'computeDrugSensitivity.R' 'computeGR.R'\n'computeIC50.R' 'computeICn.R' 'computeSlope.R'\n'computeSynergy.R' 'connectivityScore.R' 'cosinePerm.R'\n'datasets.R' 'downloadPSet.R' 'downloadSignatures.R'\n'drugDoseResponseCurve.R' 'drugPerturbationSig.R'\n'filterNoisyCurves.R' 'geneDrugPerturbation.R'\n'geneDrugSensitivity.R' 'geneDrugSensitivityPBCorr.R'\n'geneDrugSensitivityPCorr.R' 'getRawSensitivityMatrix.R'\n'globals.R' 'intersectPSets.R' 'logLogisticRegression.R'\n'matthewCor.R' 'mergePSets.R' 'methods-[.R'\n'methods-drugSensitivitySig.R' 'methods-intersect.R'\n'methods-subsetTo.R' 'methods-summarizeMolecularProfiles.R'\n'methods-summarizeSensitivityProfiles.R' 'plotPSig.R'\n'rankGeneDrugPerturbation.R' 'rankGeneDrugSensitivity.R'\n'sanityCheck.R' 'updateObject-methods.R' 'zzz.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:04 UTC",
  "RemoteUrl": "https://github.com/bioc/PharmacoGx",
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  "Packaged": {
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    "User": "root"
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  "Author": "Petr Smirnov [aut],\nChristopher Eeles [aut],\nJermiah Joseph [aut],\nZhaleh Safikhani [aut],\nMark Freeman [aut],\nFeifei Li [aut],\nBenjamin Haibe-Kains [aut, cre]",
  "Maintainer": "Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>",
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    "source": "https://www.bioconductor.org/packages/stats/bioc/PharmacoGx"
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  "_devurl": "https://github.com/bhklab/pharmacogx",
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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  "_exports": [
    ".computeAUCUnderFittedCurve",
    ".computeZIPdelta",
    ".deltaScore",
    ".logcosh",
    ".parseToRoxygen",
    ".plotProjHill",
    "amcc",
    "annotation",
    "annotation<-",
    "availablePSets",
    "checkPsetStructure",
    "computeABC",
    "computeAmax",
    "computeAUC",
    "computeBliss",
    "computeHSA",
    "computeIC50",
    "computeICn",
    "computeLoewe",
    "computeSlope",
    "computeZIP",
    "computeZIPdelta",
    "connectivityScore",
    "cosinePerm",
    "curation",
    "curation<-",
    "datasetType",
    "datasetType<-",
    "dateCreated",
    "dateCreated<-",
    "downloadPertSig",
    "downloadPSet",
    "drugDoseResponseCurve",
    "drugInfo",
    "drugInfo<-",
    "drugNames",
    "drugNames<-",
    "drugPerturbationSig",
    "drugSensitivitySig",
    "effectToDose",
    "estimateProjParams",
    "featureInfo",
    "featureInfo<-",
    "filterNoisyCurves",
    "fitTwowayZIP",
    "fNames",
    "fNames<-",
    "gwc",
    "hillCurve",
    "intersectPSet",
    "loeweCI",
    "logLogisticRegression",
    "mcc",
    "mDataNames",
    "mDataNames<-",
    "molecularProfiles",
    "molecularProfiles<-",
    "molecularProfilesSlot",
    "molecularProfilesSlot<-",
    "name",
    "name<-",
    "pertNumber",
    "pertNumber<-",
    "PharmacoSet",
    "PharmacoSet2",
    "PharmacoSig",
    "phenoInfo",
    "phenoInfo<-",
    "sampleInfo",
    "sampleInfo<-",
    "sampleNames",
    "sampleNames<-",
    "sensitivityInfo",
    "sensitivityInfo<-",
    "sensitivityMeasures",
    "sensitivityProfiles",
    "sensitivityProfiles<-",
    "sensitivityRaw",
    "sensitivityRaw<-",
    "sensNumber",
    "sensNumber<-",
    "show",
    "showSigAnnot",
    "subsetByFeature",
    "subsetBySample",
    "subsetByTreatment",
    "subsetTo",
    "summarizeMolecularProfiles",
    "summarizeSensitivityProfiles",
    "treatmentInfo",
    "treatmentInfo<-",
    "treatmentNames",
    "treatmentNames<-",
    "treatmentResponse",
    "treatmentResponse<-",
    "updateObject"
  ],
  "_datasets": [
    {
      "name": "CCLEsmall",
      "title": "Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet",
      "object": "CCLEsmall",
      "file": "CCLEsmall.rda",
      "class": [
        "PharmacoSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "CMAPsmall",
      "title": "Connectivity Map Example PharmacoSet",
      "object": "CMAPsmall",
      "file": "CMAPsmall.rda",
      "class": [
        "PharmacoSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GDSCsmall",
      "title": "Genomics of Drug Sensitivity in Cancer Example PharmacoSet",
      "object": "GDSCsmall",
      "file": "GDSCsmall.rda",
      "class": [
        "PharmacoSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HDAC_genes",
      "title": "HDAC Gene Signature",
      "object": "HDAC_genes",
      "file": "HDAC_genes.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "feature",
        "direction"
      ],
      "rows": 14,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "sub-PharmacoSet-ANY-ANY-ANY-method",
      "title": "'['",
      "topics": [
        "[,PharmacoSet,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "amcc",
      "title": "Adaptive Matthews Correlation Coefficient",
      "topics": [
        "amcc"
      ]
    },
    {
      "page": "availablePSets",
      "title": "Return a table of PharmacoSets available for download",
      "topics": [
        "availablePSets"
      ]
    },
    {
      "page": "callingWaterfall",
      "title": "Drug sensitivity calling using waterfall plots",
      "topics": [
        "callingWaterfall"
      ]
    },
    {
      "page": "CCLEsmall",
      "title": "Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet",
      "topics": [
        "CCLEsmall"
      ]
    },
    {
      "page": "checkPsetStructure",
      "title": "A function to verify the structure of a PharmacoSet",
      "topics": [
        "checkPsetStructure"
      ]
    },
    {
      "page": "CMAPsmall",
      "title": "Connectivity Map Example PharmacoSet",
      "topics": [
        "CMAPsmall"
      ]
    },
    {
      "page": "computeABC",
      "title": "Fits dose-response curves to data given by the user and returns the ABC of the fitted curves.",
      "topics": [
        "computeABC"
      ]
    },
    {
      "page": "computeAmax",
      "title": "Fits dose-response curves to data given by the user and returns the Amax of the fitted curve. Amax: 100 - viability at maximum concentarion (in fitted curve)",
      "topics": [
        "computeAmax"
      ]
    },
    {
      "page": "computeAUC",
      "title": "Computes the AUC for a Drug Dose Viability Curve",
      "topics": [
        "computeAUC"
      ]
    },
    {
      "page": "computeBliss",
      "title": "Compute Bliss Null References",
      "topics": [
        "computeBliss"
      ]
    },
    {
      "page": "computeHSA",
      "title": "Compute HSA Null References",
      "topics": [
        "computeHSA"
      ]
    },
    {
      "page": "computeICn",
      "title": "Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve",
      "topics": [
        "computeIC50",
        "computeICn"
      ]
    },
    {
      "page": "computeLoewe",
      "title": "Computes Loewe Null References",
      "topics": [
        "computeLoewe"
      ]
    },
    {
      "page": "computeSlope",
      "title": "Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input.",
      "topics": [
        "computeSlope"
      ]
    },
    {
      "page": "computeZIP",
      "title": "Computes ZIP Null References",
      "topics": [
        "computeZIP"
      ]
    },
    {
      "page": "computeZIPdelta",
      "title": "Generic to compute ZIP delta scores from an S4 object",
      "topics": [
        "computeZIPdelta"
      ]
    },
    {
      "page": "computeZIPdelta-TreatmentResponseExperiment-method",
      "title": "Compute ZIP delta score",
      "topics": [
        "computeZIPdelta,TreatmentResponseExperiment-method"
      ]
    },
    {
      "page": "connectivityScore",
      "title": "Function computing connectivity scores between two signatures",
      "topics": [
        "connectivityScore"
      ]
    },
    {
      "page": "cosinePerm",
      "title": "Cosine Permuations",
      "topics": [
        "cosinePerm"
      ]
    },
    {
      "page": "dim-PharmacoSet-method",
      "title": "Get the dimensions of a PharmacoSet",
      "topics": [
        "dim,PharmacoSet-method"
      ]
    },
    {
      "page": "downloadPertSig",
      "title": "Download Drug Perturbation Signatures",
      "topics": [
        "downloadPertSig"
      ]
    },
    {
      "page": "downloadPSet",
      "title": "Download a PharmacoSet object",
      "topics": [
        "downloadPSet"
      ]
    },
    {
      "page": "drugDoseResponseCurve",
      "title": "Plot drug response curve of a given drug and a given cell for a list of pSets (objects of the PharmacoSet class).",
      "topics": [
        "drugDoseResponseCurve"
      ]
    },
    {
      "page": "drugPerturbationSig",
      "title": "Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis.",
      "topics": [
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      ]
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      "page": "drugSensitivitySig-PharmacoSet-method",
      "title": "Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis.",
      "topics": [
        "drugSensitivitySig,PharmacoSet-method"
      ]
    },
    {
      "page": "effectToDose",
      "title": "Inverse function of Hill equation",
      "topics": [
        "effectToDose"
      ]
    },
    {
      "page": "estimateProjParams",
      "title": "Estimate the projected Hill coefficient, efficacy, and potency",
      "topics": [
        "estimateProjParams"
      ]
    },
    {
      "page": "filterNoisyCurves",
      "title": "Viability measurements in dose-reponse curves must remain stable or decrease monotonically reflecting response to the drug being tested. filterNoisyCurves flags dose-response curves that strongly violate these assumptions.",
      "topics": [
        "filterNoisyCurves"
      ]
    },
    {
      "page": "fitTwowayZIP",
      "title": "Two-way fitting for projected dose-response curve.",
      "topics": [
        "fitTwowayZIP"
      ]
    },
    {
      "page": "GDSCsmall",
      "title": "Genomics of Drug Sensitivity in Cancer Example PharmacoSet",
      "topics": [
        "GDSCsmall"
      ]
    },
    {
      "page": "geneDrugSensitivity",
      "title": "Calcualte The Gene Drug Sensitivity",
      "topics": [
        "geneDrugSensitivity"
      ]
    },
    {
      "page": "geneDrugSensitivityPBCorr",
      "title": "Calculate The Gene Drug Sensitivity",
      "topics": [
        "geneDrugSensitivityPBCorr"
      ]
    },
    {
      "page": "geneDrugSensitivityPCorr",
      "title": "Calculate The Gene Drug Sensitivity",
      "topics": [
        "geneDrugSensitivityPCorr"
      ]
    },
    {
      "page": "gwc",
      "title": "GWC Score",
      "topics": [
        "gwc"
      ]
    },
    {
      "page": "HDAC_genes",
      "title": "HDAC Gene Signature",
      "topics": [
        "HDAC_genes"
      ]
    },
    {
      "page": "hillCurve",
      "title": "4-Parameter Hill Equation for Stimuli-Response Curves",
      "topics": [
        "hillCurve"
      ]
    },
    {
      "page": "intersectPSet",
      "title": "Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user.",
      "topics": [
        "intersectPSet"
      ]
    },
    {
      "page": "loeweCI",
      "title": "Loewe Additive Combination Index (CI)",
      "topics": [
        "loeweCI"
      ]
    },
    {
      "page": "logLogisticRegression",
      "title": "Fits curves of the form E = E_inf + (1 - E_inf)/(1 + (c/EC50)^HS) to dose-response data points (c, E) given by the user and returns a vector containing estimates for HS, E_inf, and EC50.",
      "topics": [
        "logLogisticRegression"
      ]
    },
    {
      "page": "mcc",
      "title": "Compute a Mathews Correlation Coefficient",
      "topics": [
        "mcc"
      ]
    },
    {
      "page": "partialCorQUICKSTOP",
      "title": "QUICKSTOP significance testing for partial correlation",
      "topics": [
        "partialCorQUICKSTOP"
      ]
    },
    {
      "page": "PharmacoSet",
      "title": "PharmacoSet constructor",
      "topics": [
        "PharmacoSet"
      ]
    },
    {
      "page": "PharmacoSet-accessors",
      "title": "Accessing and modifying information in a 'PharmacoSet'",
      "topics": [
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        "annotation,PharmacoSet-method",
        "annotation<-",
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        "dateCreated",
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        "featureInfo<-,PharmacoSet,character,DataFrame-method",
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        "fNames,PharmacoSet,character-method",
        "fNames<-",
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        "mDataNames",
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        "mDataNames<-",
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        "mDataNames<-,PharmacoSet-method",
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        "molecularProfiles<-,PharmacoSet,missing,missing,list-method",
        "molecularProfiles<-,PharmacoSet,missing,missing,MutliAssayExperiment-method",
        "molecularProfilesSlot",
        "molecularProfilesSlot,PharmacoSet-method",
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        "molecularProfilesSlot<-,PharmacoSet,list_OR_MAE-method",
        "molecularProfilesSlot<-PharmacoSet,MultiAssayExperiment-method",
        "moleculerProfilesSlot,PharmacoSet-method",
        "name",
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        "phenoInfo<-,PharmacoSet,character,DataFrame-method",
        "sampleInfo",
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      "page": "PharmacoSet-class",
      "title": "A Class to Contain PharmacoGenomic datasets together with their curations",
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        "subsetBySample,PharmacoSet-method",
        "subsetByTreatment",
        "subsetByTreatment,PharmacoSet-method"
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    {
      "page": "PharmacoSet2",
      "title": "Make a CoreSet with the updated class structure",
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    {
      "page": "PharmacoSig",
      "title": "Contructor for the PharmacoSig S4 class",
      "topics": [
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    {
      "page": "plot.PharmacoSig",
      "title": "Plots a PharmacoSig object into a Volcano Plot",
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    {
      "page": "show-PharmacoSet-method",
      "title": "Show a PharamcoSet",
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        "show,PharmacoSet-method"
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      "page": "show-PharmacoSig-method",
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        "show,PharmacoSig-method"
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      "page": "showSigAnnot-PharmacoSig-method",
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      "page": "subsetTo-PharmacoSet-method",
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      "page": "summarizeSensitivityProfiles-PharmacoSet-method",
      "title": "Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table",
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    {
      "page": "updateObject-PharmacoSet-method",
      "title": "Update the PharmacoSet class after changes in it struture or API",
      "topics": [
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      "title": "PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets",
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      "title": "PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets",
      "author": "Petr Smirnov, Christopher Eeles, Zhaleh Safikhani, Benjamin Haibe-Kains",
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