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  "_homeurl": "https://github.com/bhklab/pharmacogx",
  "_realowner": "bioc",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.6",
      "date": "2015-07-24"
    },
    {
      "version": "1.1.2",
      "date": "2015-11-15"
    },
    {
      "version": "1.1.4",
      "date": "2016-01-08"
    },
    {
      "version": "1.1.5",
      "date": "2016-05-17"
    },
    {
      "version": "1.1.6",
      "date": "2016-06-10"
    }
  ],
  "_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": [
        "drugPerturbationSig"
      ]
    },
    {
      "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": [
        "annotation",
        "annotation,PharmacoSet-method",
        "annotation<-",
        "annotation<-,PharmacoSet,list-method",
        "cellInfo",
        "cellInfo,PharmacoSet-method",
        "cellInfo<-",
        "cellInfo<-,PharmacoSet,data.frame-method",
        "cellName,PharmacoSet-method",
        "cellNames",
        "cellNames<-",
        "cellNames<-,PharmacoSet,list-method",
        "curation",
        "curation,PharmacoSet-method",
        "curation<-",
        "curation<-,PharmacoSet,list-method",
        "datasetType",
        "datasetType,PharmacoSet-method",
        "datasetType<-",
        "datasetType<-,PharmacoSet,character-method",
        "dateCreated",
        "dateCreated,PharmacoSet-method",
        "dateCreated<-",
        "dateCreated<-,PharmacoSet,character-method",
        "dateCreated<-,PharmacoSet-method",
        "drugInfo",
        "drugInfo<-",
        "drugNames",
        "drugNames<-",
        "featureInfo",
        "featureInfo,PharmacoSet-method",
        "featureInfo<-",
        "featureInfo<-,PharmacoSet,character,data.frame-method",
        "featureInfo<-,PharmacoSet,character,DataFrame-method",
        "fNames",
        "fNames,PharmacoSet,character-method",
        "fNames<-",
        "fNames<-,PharmacoSet,character,character-method",
        "mDataNames",
        "mDataNames,PharmacoSet-method",
        "mDataNames<-",
        "mDataNames<-,PharmacoSet,ANY-method",
        "mDataNames<-,PharmacoSet-method",
        "molecularProfiles",
        "molecularProfiles,PharmacoSet-method",
        "molecularProfiles<-",
        "molecularProfiles<-,PharmacoSet,character,character,matrix-method",
        "molecularProfiles<-,PharmacoSet,character,missing,matrix-method",
        "molecularProfiles<-,PharmacoSet,missing,missing,list-method",
        "molecularProfiles<-,PharmacoSet,missing,missing,MutliAssayExperiment-method",
        "molecularProfilesSlot",
        "molecularProfilesSlot,PharmacoSet-method",
        "molecularProfilesSlot<-",
        "molecularProfilesSlot<-,PharmacoSet,list-method",
        "molecularProfilesSlot<-,PharmacoSet,list_OR_MAE-method",
        "molecularProfilesSlot<-PharmacoSet,MultiAssayExperiment-method",
        "moleculerProfilesSlot,PharmacoSet-method",
        "name",
        "name,PharmacoSet-method",
        "name<-",
        "name<-,PharmacoSet,character-method",
        "name<-,PharmacoSet-method",
        "pertNumber",
        "pertNumber,PharmacoSet-method",
        "pertNumber<-",
        "pertNumber<-,PharmacoSet,array-method",
        "PharmacoSet-accessors",
        "phenoInfo",
        "phenoInfo,PharmacoSet,character-method",
        "phenoInfo<-",
        "phenoInfo<-,PharmacoSet,character,data.frame-method",
        "phenoInfo<-,PharmacoSet,character,DataFrame-method",
        "sampleInfo",
        "sampleInfo,PharmacoSet-method",
        "sampleInfo<-",
        "sampleInfo<-,PharmacoSet,data.frame-method",
        "sampleName,PharmacoSet-method",
        "sampleNames",
        "sampleNames,PharmacoSet-method",
        "sampleNames<-",
        "sampleNames<-,PharmacoSet,character-method",
        "sampleNames<-,PharmacoSet,list-method",
        "sensitivityInfo,PharmacoSet,character-method",
        "sensitivityInfo,PharmacoSet,missing-method",
        "sensitivityInfo,PharmacoSet-method",
        "sensitivityInfo<-,PharmacoSet,data.frame-method",
        "sensitivityInfo<-,PharmacoSet,missing,data.frame-method",
        "sensitivityMeasures,PharmacoSet-method",
        "sensitivityMeasures<-,PharmacoSet,character-method",
        "sensitivityProfiles,PharmacoSet-method",
        "sensitivityProfiles<-,PharmacoSet,data.frame-method",
        "sensitivityRaw,PharmacoSet-method",
        "sensitivityRaw<-,PharmacoSet,array-method",
        "sensitivitySlot",
        "sensitivitySlot<-",
        "sensitvityInfo<-,PharmacoSet,character,data.frame-method",
        "sensNumber",
        "sensNumber,PharmacoSet-method",
        "sensNumber<-",
        "sensNumber<-,PharmacoSet,matrix-method",
        "treamentResponse<-,PharmacoSet,list-method",
        "treatmentInfo",
        "treatmentInfo,PharmacoSet-method",
        "treatmentInfo<-",
        "treatmentInfo<-,PharmacoSet,data.frame-method",
        "treatmentNames",
        "treatmentNames,PharmacoSet-method",
        "treatmentNames<-",
        "treatmentNames<-,PharmacoSet,character-method",
        "treatmentResponse",
        "treatmentResponse,PharmacoSet-method",
        "treatmentResponse<-",
        "treatmentResponse<-,PharmacoSet,list_OR_LongTable-method",
        "treatmentResponse<-,PharmacoSet,LongTable-method"
      ]
    },
    {
      "page": "PharmacoSet-class",
      "title": "A Class to Contain PharmacoGenomic datasets together with their curations",
      "topics": [
        ".PharmacoSet",
        "PharmacoSet-class"
      ]
    },
    {
      "page": "PharmacoSet-utils",
      "title": "Utility methods for a 'PharmacoSet' object.",
      "topics": [
        "PharmacoSet-utils",
        "subsetByFeature",
        "subsetByFeature,PharmacoSet-method",
        "subsetBySample",
        "subsetBySample,CoreSet-method",
        "subsetBySample,PharmacoSet-method",
        "subsetByTreatment",
        "subsetByTreatment,PharmacoSet-method"
      ]
    },
    {
      "page": "PharmacoSet2",
      "title": "Make a CoreSet with the updated class structure",
      "topics": [
        "PharmacoSet2"
      ]
    },
    {
      "page": "PharmacoSig",
      "title": "Contructor for the PharmacoSig S4 class",
      "topics": [
        "PharmacoSig"
      ]
    },
    {
      "page": "plot.PharmacoSig",
      "title": "Plots a PharmacoSig object into a Volcano Plot",
      "topics": [
        "plot.PharmacoSig"
      ]
    },
    {
      "page": "show-PharmacoSet-method",
      "title": "Show a PharamcoSet",
      "topics": [
        "show,PharmacoSet-method"
      ]
    },
    {
      "page": "show-PharmacoSig-method",
      "title": "Show PharmacoGx Signatures",
      "topics": [
        "show,PharmacoSig-method"
      ]
    },
    {
      "page": "showSigAnnot-PharmacoSig-method",
      "title": "Show the Annotations of a signature object",
      "topics": [
        "showSigAnnot,PharmacoSig-method"
      ]
    },
    {
      "page": "subsetTo-PharmacoSet-method",
      "title": "A function to subset a PharmacoSet to data containing only specified drugs, cells and genes",
      "topics": [
        "subsetTo,PharmacoSet-method"
      ]
    },
    {
      "page": "summarizeSensitivityProfiles-PharmacoSet-method",
      "title": "Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table",
      "topics": [
        "summarizeSensitivityProfiles,PharmacoSet-method"
      ]
    },
    {
      "page": "updateObject-PharmacoSet-method",
      "title": "Update the PharmacoSet class after changes in it struture or API",
      "topics": [
        "updateObject,PharmacoSet-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/PharmacoGx/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "base64enc",
    "bench",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocParallel",
    "bitops",
    "boot",
    "bslib",
    "BumpyMatrix",
    "cachem",
    "caTools",
    "celestial",
    "checkmate",
    "cli",
    "cluster",
    "codetools",
    "commonmark",
    "coop",
    "CoreGx",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "data.table",
    "DelayedArray",
    "digest",
    "downloader",
    "dplyr",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fastmatch",
    "fgsea",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "limma",
    "lsa",
    "magicaxis",
    "magrittr",
    "mapproj",
    "maps",
    "marray",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "MultiAssayExperiment",
    "NISTunits",
    "otel",
    "piano",
    "pillar",
    "pkgconfig",
    "plotrix",
    "plyr",
    "pracma",
    "profmem",
    "promises",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "relations",
    "reshape2",
    "rlang",
    "rmarkdown",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "sets",
    "shiny",
    "shinydashboard",
    "shinyjs",
    "slam",
    "sm",
    "snow",
    "SnowballC",
    "sourcetools",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "visNetwork",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "CreatingPharmacoSet.Rmd",
      "filename": "CreatingPharmacoSet.html",
      "title": "PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets",
      "author": "Petr Smirnov, Christopher Eeles, Zhaleh Safikhani, Benjamin Haibe-Kains",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "PharmacoSet Structure",
        "sample",
        "treatment",
        "curation:",
        "molecularProfiles:",
        "datasetType",
        "treatmentResponse:",
        "New in PharmacoGx 2.0",
        "Old in PharmacoGx 1.0",
        "perturbation:",
        "annotation",
        "Creating the PharmacoSet",
        "PharmacoGx 2.0",
        "PharmacoGx 1.0"
      ],
      "created": "2020-04-26 17:32:16",
      "modified": "2024-04-08 20:19:36",
      "commits": 8
    },
    {
      "source": "DetectingDrugSynergyAndAntagonism.Rmd",
      "filename": "DetectingDrugSynergyAndAntagonism.html",
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