{
  "_id": "6a1af5fe1d7bb097a09f98f2",
  "Package": "ToxicoGx",
  "Type": "Package",
  "Title": "Analysis of Large-Scale Toxico-Genomic Data",
  "Version": "2.17.0",
  "Date": "2023-03-08",
  "Authors@R": "c(\nperson(\"Sisira\",\"Nair\", email = \"sisira.nair@uhnresearch.ca\",\nrole = c(\"aut\")),\nperson(\"Esther\",\"Yoo\", email = \"yk.yoo@mail.utoronto.ca\",\nrole = c(\"aut\")),\nperson(\"Christopher\",\"Eeles\", email = \"christopher.eeles@uhnresearch.ca\",\nrole = c(\"aut\")),\nperson(\"Amy\", \"Tang\", email = \"amy.tang@queensu.ca\",\nrole = c(\"aut\")),\nperson(\"Nehme\", \"El-Hachem\", email = \"hachemn@gmail.com\",\nrole = c(\"aut\")),\nperson(\"Petr\",\"Smirnov\", email = \"petr.smirnov@uhnresearch.ca\",\nrole = c(\"aut\")),\nperson(\"Jermiah\",\"Joseph\", email = \"jermiah.joseph@uhn.ca\",\nrole = c(\"aut\")),\nperson(\"Benjamin\",\"Haibe-Kains\", email = \"benjamin.haibe.kains@utoronto.ca\",\nrole = c(\"aut\",\"cre\"))\n)",
  "Description": "Contains a set of functions to perform large-scale\nanalysis of toxicogenomic data, providing a standardized data\nstructure to hold information relevant to annotation,\nvisualization and statistical analysis of toxicogenomic data.",
  "License": "MIT + file LICENSE",
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  "Collate": "'LogLogisticRegression.R' 'SanityCheck.R' 'allGenerics.R'\n'ToxicoSet-class.R' 'ToxicoSet-accessors.R' 'class-signature.R'\n'columnsAsCharacter.R' 'computeAUC.R'\n'computeDrugSensitivity.R' 'computeIC50.R' 'computeICn.R'\n'dataset.R' 'downloadTSet.R' 'drugGeneResponseCurve.R'\n'drugPerturbationSig.R' 'drugTimeResponseCurve.R'\n'geneDrugPerturbation.R' 'geneDrugSensitivity.R' 'globals.R'\n'methods-computeLimmaDiffExpr.R' 'methods-subsetTo.R'\n'paramErrorChecker.R' 'paramMissingHandler.R'\n'paramMissingHandlerTests.R' 'rankGeneDrugPerturbation.R'\n'rankGeneDrugSensitivity.R' 'summarizeMolecularProfiles.R'\n'summarizeSensitivityProfiles.R' 'updateObject-methods.R'\n'utilities.R' 'zzz.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:01 UTC",
  "RemoteUrl": "https://github.com/bioc/ToxicoGx",
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  "Packaged": {
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  "Author": "Sisira Nair [aut],\nEsther Yoo [aut],\nChristopher Eeles [aut],\nAmy Tang [aut],\nNehme El-Hachem [aut],\nPetr Smirnov [aut],\nJermiah Joseph [aut],\nBenjamin Haibe-Kains [aut, cre]",
  "Maintainer": "Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>",
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  "_published": "2026-05-30T14:36:46.026Z",
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    "pharmacogenetics",
    "pharmacogenomics",
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_exports": [
    ".convertTsetMolecularProfilesToSE",
    "annotation",
    "annotation<-",
    "availableTSets",
    "checkTSetStructure",
    "computeAUC",
    "computeIC50",
    "computeICn",
    "computeLimmaDiffExpr",
    "curation",
    "curation<-",
    "datasetType",
    "datasetType<-",
    "dateCreated",
    "dateCreated<-",
    "downloadTSet",
    "drugGeneResponseCurve",
    "drugInfo",
    "drugInfo<-",
    "drugNames",
    "drugNames<-",
    "drugPerturbationSig",
    "drugTimeResponseCurve",
    "featureInfo",
    "featureInfo<-",
    "fNames",
    "fNames<-",
    "geneDrugPerturbation",
    "logLogisticRegression",
    "mDataNames",
    "mDataNames<-",
    "molecularProfiles",
    "molecularProfiles<-",
    "molecularProfilesSlot",
    "molecularProfilesSlot<-",
    "name",
    "name<-",
    "pertNumber",
    "pertNumber<-",
    "phenoInfo",
    "phenoInfo<-",
    "sampleInfo",
    "sampleInfo<-",
    "sampleNames",
    "sampleNames<-",
    "sensitivityInfo",
    "sensitivityInfo<-",
    "sensitivityMeasures",
    "sensitivityProfiles",
    "sensitivityProfiles<-",
    "sensitivityRaw",
    "sensitivityRaw<-",
    "sensNumber",
    "sensNumber<-",
    "show",
    "showSigAnnot",
    "subsetTo",
    "summarizeMolecularProfiles",
    "summarizeSensitivityProfiles",
    "ToxicoSet",
    "ToxicoSig",
    "treatmentInfo",
    "treatmentInfo<-",
    "treatmentNames",
    "treatmentNames<-",
    "treatmentResponse",
    "treatmentResponse<-",
    "updateObject"
  ],
  "_datasets": [
    {
      "name": "HCC_sig",
      "title": "HCC_sig dataset",
      "object": "HCC_sig",
      "class": [
        "data.frame"
      ],
      "fields": [
        "feature",
        "direction"
      ],
      "rows": 7158,
      "table": true,
      "tojson": true
    },
    {
      "name": "TGGATESsmall",
      "title": "TGGATESsmall dataset",
      "object": "TGGATESsmall",
      "class": [
        "ToxicoSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "sub-ToxicoSet-ANY-ANY-ANY-method",
      "title": "'['",
      "topics": [
        "[,ToxicoSet,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "availableTSets",
      "title": "Return a table of ToxicoSets available for download",
      "topics": [
        "availableTSets"
      ]
    },
    {
      "page": "checkTSetStructure",
      "title": "A function to verify the structure of a ToxicoSet",
      "topics": [
        "checkTSetStructure"
      ]
    },
    {
      "page": "computeAUC",
      "title": "Computes the AUC for a Drug Dose Viability Curve",
      "topics": [
        "computeAUC"
      ]
    },
    {
      "page": "computeICn",
      "title": "Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve",
      "topics": [
        "computeIC50",
        "computeICn"
      ]
    },
    {
      "page": "computeLimmaDiffExpr",
      "title": "Generic method for performing differential expression analysis on an S4 object using the limma package",
      "topics": [
        "computeLimmaDiffExpr"
      ]
    },
    {
      "page": "computeLimmaDiffExpr-ToxicoSet-method",
      "title": "Conduct differential expression analysis using the limma R pacakge",
      "topics": [
        "computeLimmaDiffExpr,ToxicoSet-method"
      ]
    },
    {
      "page": "dim-ToxicoSet-method",
      "title": "Get the dimensions of a ToxicoSet",
      "topics": [
        "dim,ToxicoSet-method"
      ]
    },
    {
      "page": "downloadTSet",
      "title": "Download a ToxicoSet object",
      "topics": [
        "downloadTSet"
      ]
    },
    {
      "page": "drugGeneResponseCurve",
      "title": "Compares gene expression for a specificed set of features over specific drug dosages vs time",
      "topics": [
        "drugGeneResponseCurve"
      ]
    },
    {
      "page": "drugPerturbationSig",
      "title": "Drug perturbation analysis",
      "topics": [
        "drugPerturbationSig"
      ]
    },
    {
      "page": "drugTimeResponseCurve",
      "title": "Compares viabilities at a given dose over different experimental durations",
      "topics": [
        "drugTimeResponseCurve"
      ]
    },
    {
      "page": "HCC_sig",
      "title": "HCC_sig dataset",
      "topics": [
        "HCC_sig"
      ]
    },
    {
      "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": "show-ToxicoSet-method",
      "title": "Show a ToxicoSet",
      "topics": [
        "show,ToxicoSet-method"
      ]
    },
    {
      "page": "show-ToxicoSig-method",
      "title": "Show ToxicoGx Signatures",
      "topics": [
        "show,ToxicoSig-method"
      ]
    },
    {
      "page": "showSigAnnot",
      "title": "Show the Annotations of a signature object",
      "topics": [
        "showSigAnnot"
      ]
    },
    {
      "page": "subsetTo",
      "title": "A function to subset a ToxicoSet to data containing only specified drugs, cells and genes",
      "topics": [
        "subsetTo"
      ]
    },
    {
      "page": "summarizeMolecularProfiles",
      "title": "Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition.",
      "topics": [
        "summarizeMolecularProfiles"
      ]
    },
    {
      "page": "summarizeSensitivityProfiles",
      "title": "Takes the sensitivity data from a ToxicoSet, and summarises them into a drug vs cell line table",
      "topics": [
        "summarizeSensitivityProfiles"
      ]
    },
    {
      "page": "TGGATESsmall",
      "title": "TGGATESsmall dataset",
      "topics": [
        "TGGATESsmall"
      ]
    },
    {
      "page": "ToxicoSet",
      "title": "ToxicoSet constructor",
      "topics": [
        "ToxicoSet"
      ]
    },
    {
      "page": "ToxicoSet-accessors",
      "title": "Accessing and modifying information in a 'CoreSet'",
      "topics": [
        "annotation",
        "annotation,ToxicoSet-method",
        "annotation<-",
        "annotation<-,ToxicoSet,list-method",
        "cellInfo",
        "cellInfo,ToxicoSet-method",
        "cellInfo<-",
        "cellInfo<-,ToxicoSet,data.frame-method",
        "cellName,ToxicoSet-method",
        "cellNames",
        "cellNames<-",
        "cellNames<-,ToxicoSet,list-method",
        "curation",
        "curation,ToxicoSet-method",
        "curation<-",
        "curation<-,ToxicoSet,list-method",
        "datasetType",
        "datasetType,ToxicoSet-method",
        "datasetType<-",
        "datasetType<-,ToxicoSet,character-method",
        "dateCreated",
        "dateCreated,ToxicoSet-method",
        "dateCreated<-",
        "dateCreated<-,ToxicoSet,character-method",
        "dateCreated<-,ToxicoSet-method",
        "drugInfo",
        "drugInfo<-",
        "drugNames",
        "drugNames<-",
        "featureInfo",
        "featureInfo,ToxicoSet-method",
        "featureInfo<-",
        "featureInfo<-,ToxicoSet,character,data.frame-method",
        "featureInfo<-,ToxicoSet,character,DataFrame-method",
        "fNames",
        "fNames,ToxicoSet,character-method",
        "fNames<-",
        "fNames<-,ToxicoSet,character,character-method",
        "mDataNames",
        "mDataNames,ToxicoSet-method",
        "mDataNames<-",
        "mDataNames<-,ToxicoSet,ANY-method",
        "mDataNames<-,ToxicoSet-method",
        "molecularProfiles",
        "molecularProfiles,ToxicoSet-method",
        "molecularProfiles<-",
        "molecularProfiles<-,ToxicoSet,character,character,matrix-method",
        "molecularProfiles<-,ToxicoSet,character,missing,matrix-method",
        "molecularProfiles<-,ToxicoSet,missing,missing,list-method",
        "molecularProfiles<-,ToxicoSet,missing,missing,MutliAssayExperiment-method",
        "molecularProfilesSlot",
        "molecularProfilesSlot,ToxicoSet-method",
        "molecularProfilesSlot<-",
        "molecularProfilesSlot<-,ToxicoSet,list-method",
        "molecularProfilesSlot<-,ToxicoSet,list_OR_MAE-method",
        "molecularProfilesSlot<-ToxicoSet,MultiAssayExperiment-method",
        "moleculerProfilesSlot,ToxicoSet-method",
        "name",
        "name,ToxicoSet-method",
        "name<-",
        "name<-,ToxicoSet,character-method",
        "name<-,ToxicoSet-method",
        "pertNumber",
        "pertNumber,ToxicoSet-method",
        "pertNumber<-",
        "pertNumber<-,ToxicoSet,array-method",
        "phenoInfo",
        "phenoInfo,ToxicoSet,character-method",
        "phenoInfo<-",
        "phenoInfo<-,ToxicoSet,character,data.frame-method",
        "phenoInfo<-,ToxicoSet,character,DataFrame-method",
        "sampleInfo",
        "sampleInfo,ToxicoSet-method",
        "sampleInfo<-",
        "sampleInfo<-,ToxicoSet,data.frame-method",
        "sampleName,ToxicoSet-method",
        "sampleNames",
        "sampleNames,ToxicoSet-method",
        "sampleNames<-",
        "sampleNames<-,ToxicoSet,character-method",
        "sampleNames<-,ToxicoSet,list-method",
        "sensitivityInfo,ToxicoSet,character-method",
        "sensitivityInfo,ToxicoSet,missing-method",
        "sensitivityInfo,ToxicoSet-method",
        "sensitivityInfo<-,ToxicoSet,data.frame-method",
        "sensitivityInfo<-,ToxicoSet,missing,data.frame-method",
        "sensitivityMeasures,ToxicoSet-method",
        "sensitivityMeasures<-,ToxicoSet,character-method",
        "sensitivityProfiles,ToxicoSet-method",
        "sensitivityProfiles<-,ToxicoSet,data.frame-method",
        "sensitivityRaw,ToxicoSet-method",
        "sensitivityRaw<-,ToxicoSet,array-method",
        "sensitivitySlot",
        "sensitivitySlot<-",
        "sensitvityInfo<-,ToxicoSet,character,data.frame-method",
        "sensNumber",
        "sensNumber,ToxicoSet-method",
        "sensNumber<-",
        "sensNumber<-,ToxicoSet,matrix-method",
        "ToxicoSet-accessors",
        "treamentResponse<-,ToxicoSet,list-method",
        "treatmentInfo",
        "treatmentInfo,ToxicoSet-method",
        "treatmentInfo<-",
        "treatmentInfo<-,ToxicoSet,data.frame-method",
        "treatmentNames",
        "treatmentNames,ToxicoSet-method",
        "treatmentNames<-",
        "treatmentNames<-,ToxicoSet,character-method",
        "treatmentResponse",
        "treatmentResponse,ToxicoSet-method",
        "treatmentResponse<-",
        "treatmentResponse<-,ToxicoSet,list_OR_LongTable-method",
        "treatmentResponse<-,ToxicoSet,LongTable-method"
      ]
    },
    {
      "page": "ToxicoSet-class",
      "title": "Class to contain Toxico-genomic Data",
      "topics": [
        ".ToxicoSet",
        "ToxicoSet-class"
      ]
    },
    {
      "page": "updateObject-ToxicoSet-method",
      "title": "Update the ToxicoSet class after changes in it struture or API",
      "topics": [
        "updateObject,ToxicoSet-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ToxicoGx/raw/HEAD/README.md",
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