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    "gtoxCalcVmad",
    "gtoxCode2CASN",
    "gtoxConf",
    "gtoxConfDefault",
    "gtoxConfList",
    "gtoxConfLoad",
    "gtoxConfReset",
    "gtoxConfSave",
    "gtoxFit",
    "gtoxHillACXX",
    "gtoxHillConc",
    "gtoxHillVal",
    "gtoxImportThermoDB",
    "gtoxListFlds",
    "gtoxLoadAcid",
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    "gtoxLoadChem",
    "gtoxLoadClib",
    "gtoxLoadData",
    "gtoxLoadVehicle",
    "gtoxLoadVmad",
    "gtoxLoadWaid",
    "gtoxMakeAeidPlts",
    "gtoxMthdAssign",
    "gtoxMthdClear",
    "gtoxMthdList",
    "gtoxMthdLoad",
    "gtoxObjCnst",
    "gtoxObjGnls",
    "gtoxObjHill",
    "gtoxPlotErrBar",
    "gtoxPlotFitc",
    "gtoxPlotFits",
    "gtoxPlotM4ID",
    "gtoxPlotPie",
    "gtoxPlotPieLgnd",
    "gtoxPlotPlate",
    "gtoxPlotWin",
    "gtoxPrepOtpt",
    "gtoxQuery",
    "gtoxRegister",
    "gtoxReport",
    "gtoxRun",
    "gtoxSendQuery",
    "gtoxSetWllq",
    "gtoxSubsetChid",
    "gtoxUpdate",
    "gtoxWriteData",
    "loadAnnot",
    "lu",
    "lw",
    "prepareDatForDB"
  ],
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    {
      "page": "assignDefaultMthds",
      "title": "Assign default processing methods",
      "topics": [
        "assignDefaultMthds"
      ]
    },
    {
      "page": "buildAssayTab",
      "title": "Prepare assay table mapping info",
      "topics": [
        "buildAssayTab"
      ]
    },
    {
      "page": "config_funcs",
      "title": "Functions for configuring the gtox package",
      "topics": [
        "Configure functions",
        "gtoxConf",
        "gtoxConfDefault",
        "gtoxConfList",
        "gtoxConfLoad",
        "gtoxConfReset",
        "gtoxConfSave"
      ]
    },
    {
      "page": "deleteStudy",
      "title": "Completely remove all data for a study",
      "topics": [
        "deleteStudy"
      ]
    },
    {
      "page": "exportResultForToxpiGUI",
      "title": "Create the result table for the asi in input",
      "topics": [
        "exportResultForToxpiGUI"
      ]
    },
    {
      "page": "exportResultTable",
      "title": "Create the result table for the asi in input",
      "topics": [
        "exportResultTable"
      ]
    },
    {
      "page": "glCheckInput",
      "title": "Check validity of input file",
      "topics": [
        "glCheckInput"
      ]
    },
    {
      "page": "glComputeToxInd",
      "title": "Create toxicological indicator values for all chemicals in input",
      "topics": [
        "glComputeToxInd"
      ]
    },
    {
      "page": "glLoadInput",
      "title": "Check validity of input file",
      "topics": [
        "glLoadInput"
      ]
    },
    {
      "page": "glPlotPie",
      "title": "Pie chart for Minimal Effective Concentrations (MEC) and AC50 plot",
      "topics": [
        "glPlotPie"
      ]
    },
    {
      "page": "glPlotPieLogo",
      "title": "plot package logo",
      "topics": [
        "glPlotPieLogo"
      ]
    },
    {
      "page": "glPlotPosCtrl",
      "title": "Box plot for positive control check",
      "topics": [
        "glPlotPosCtrl"
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    },
    {
      "page": "glPlotPosCtrlMEC",
      "title": "Box plot for positive control check",
      "topics": [
        "glPlotPosCtrlMEC"
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    {
      "page": "glPlotStat",
      "title": "Box plot for Minimal Effective Concentrations (MEC) and AC50 plot",
      "topics": [
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    },
    {
      "page": "glPlotToxInd",
      "title": "Plot toxicological indicator values for all chemicals in input",
      "topics": [
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      ]
    },
    {
      "page": "gtoxAddModel",
      "title": "Draw a gtox Model onto an exisiting plot",
      "topics": [
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      ]
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    {
      "page": "gtoxAICProb",
      "title": "Calculate the AIC probabilities",
      "topics": [
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    },
    {
      "page": "gtoxCalcVmad",
      "title": "Calculate and update the assay endpoint cutoff values",
      "topics": [
        "gtoxCalcVmad"
      ]
    },
    {
      "page": "gtoxCode2CASN",
      "title": "Convert chemical code to CAS Registry Number",
      "topics": [
        "gtoxCode2CASN"
      ]
    },
    {
      "page": "gtoxFit",
      "title": "Fit the data with the constant, hill, and gain-loss models",
      "topics": [
        "gtoxFit"
      ]
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    {
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      "title": "Functions to solve the Hill model",
      "topics": [
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        "gtoxHillConc",
        "gtoxHillVal",
        "Hill model utilites"
      ]
    },
    {
      "page": "gtoxImportThermoDB",
      "title": "Import data from ThermoDB by study ID",
      "topics": [
        "gtoxImportThermoDB"
      ]
    },
    {
      "page": "gtoxListFlds",
      "title": "Load the field names for a table",
      "topics": [
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      ]
    },
    {
      "page": "gtoxLoadApid",
      "title": "Load assay plate information",
      "topics": [
        "gtoxLoadApid"
      ]
    },
    {
      "page": "gtoxLoadChem",
      "title": "Load sample/chemical information",
      "topics": [
        "gtoxLoadChem"
      ]
    },
    {
      "page": "gtoxLoadClib",
      "title": "Load chemical library information",
      "topics": [
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      ]
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    {
      "page": "gtoxLoadData",
      "title": "Load gtox data",
      "topics": [
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      ]
    },
    {
      "page": "gtoxLoadVehicle",
      "title": "Load vehicle information",
      "topics": [
        "gtoxLoadVehicle"
      ]
    },
    {
      "page": "gtoxLoadVmad",
      "title": "Load cutoff values for assay endpoints",
      "topics": [
        "gtoxLoadVmad"
      ]
    },
    {
      "page": "gtoxLoadWaid",
      "title": "Load well annotation information",
      "topics": [
        "gtoxLoadWaid"
      ]
    },
    {
      "page": "gtoxMakeAeidPlts",
      "title": "Create a .pdf with dose-response plots",
      "topics": [
        "gtoxMakeAeidPlts"
      ]
    },
    {
      "page": "mthd_funcs",
      "title": "Functions for managing processing methods",
      "topics": [
        "gtoxMthdAssign",
        "gtoxMthdClear",
        "gtoxMthdList",
        "gtoxMthdLoad",
        "Method functions"
      ]
    },
    {
      "page": "gtoxPlotErrBar",
      "title": "Create error bar plots",
      "topics": [
        "gtoxPlotErrBar"
      ]
    },
    {
      "page": "gtoxPlotFitc",
      "title": "Plot the fit category tree",
      "topics": [
        "gtoxPlotFitc"
      ]
    },
    {
      "page": "gtoxPlotFits",
      "title": "Plot summary fits based on fit and dose-response data",
      "topics": [
        "gtoxPlotFits"
      ]
    },
    {
      "page": "gtoxPlotM4ID",
      "title": "Plot fit summary plot by m4id",
      "topics": [
        "gtoxPlotM4ID"
      ]
    },
    {
      "page": "gtoxPlotPie",
      "title": "Create piechart plots",
      "topics": [
        "gtoxPlotPie"
      ]
    },
    {
      "page": "gtoxPlotPieLgnd",
      "title": "Create piechart plot legend",
      "topics": [
        "gtoxPlotPieLgnd"
      ]
    },
    {
      "page": "gtoxPlotPlate",
      "title": "Plot plate heatmap",
      "topics": [
        "gtoxPlotPlate"
      ]
    },
    {
      "page": "gtoxPlotWin",
      "title": "Create winning curve plots",
      "topics": [
        "gtoxPlotWin"
      ]
    },
    {
      "page": "gtoxPrepOtpt",
      "title": "Map assay/chemcial ID values to annotation information",
      "topics": [
        "gtoxPrepOtpt"
      ]
    },
    {
      "page": "query_funcs",
      "title": "Wrappers for sending queries and fetching results",
      "topics": [
        "gtoxQuery",
        "gtoxSendQuery",
        "Query functions"
      ]
    },
    {
      "page": "rgstr_funcs",
      "title": "Functions for registering & updating annotation information",
      "topics": [
        "gtoxRegister",
        "gtoxUpdate",
        "Register/update annotation"
      ]
    },
    {
      "page": "gtoxReport",
      "title": "Generate a report",
      "topics": [
        "gtoxReport"
      ]
    },
    {
      "page": "gtoxRun",
      "title": "Perform data processing",
      "concept": [
        "data processing functions"
      ],
      "topics": [
        "gtoxRun"
      ]
    },
    {
      "page": "gtoxSetWllq",
      "title": "Change the well quality for a vector of lvl 0 IDs",
      "topics": [
        "gtoxSetWllq"
      ]
    },
    {
      "page": "gtoxSubsetChid",
      "title": "Subset level 5 data to a single sample per chemical",
      "topics": [
        "gtoxSubsetChid"
      ]
    },
    {
      "page": "gtoxWriteData",
      "title": "Write screening data into the gtox databases",
      "topics": [
        "gtoxWriteData"
      ]
    },
    {
      "page": "assay_funcs",
      "title": "Functions for loading assay information",
      "topics": [
        "gtoxLoadAcid",
        "gtoxLoadAeid",
        "gtoxLoadAid",
        "gtoxLoadAsid",
        "Load assay information"
      ]
    },
    {
      "page": "loadAnnot",
      "title": "Register the annotations provided by GUI",
      "topics": [
        "loadAnnot"
      ]
    },
    {
      "page": "lu",
      "title": "Abbreviation for 'length(unique(x))'",
      "concept": [
        "gtox abbreviations"
      ],
      "topics": [
        "lu"
      ]
    },
    {
      "page": "lw",
      "title": "Abbreviation for 'length(which(x))'",
      "concept": [
        "gtox abbreviations"
      ],
      "topics": [
        "lw"
      ]
    },
    {
      "page": "Models",
      "title": "Model objective functions",
      "topics": [
        "gtoxObjCnst",
        "gtoxObjGnls",
        "gtoxObjHill",
        "Models"
      ]
    },
    {
      "page": "prepareDatForDB",
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      "title": "GladiaTOX: R Package for Processing High Content Screening data",
      "author": "Vincenzo Belcastro, Stephane Cano, Florian Martin",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation and package load",
        "Database configuration",
        "Deployed database",
        "Data and metadata for vignette",
        "plate: plate metadata",
        "chnmap: assay metadata and channel mapping",
        "dat: image quantification raw data",
        "Database loading",
        "Register study info in database",
        "Load raw data in database",
        "Quality control: data processing and reporting",
        "Compute the noise band",
        "Quality control report",
        "Data masking",
        "Data processing and reporting",
        "Process data",
        "Data reporting",
        "Additional reporting plots",
        "Session Info"
      ],
      "created": "2019-04-11 07:21:18",
      "modified": "2023-09-15 09:36:12",
      "commits": 4
    }
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  "_indexed": true,
  "_nocasepkg": "gladiatox",
  "_universes": [
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    "philipmorrisintl"
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