{
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  "Package": "RadioGx",
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  "Title": "Analysis of Large-Scale Radio-Genomic Data",
  "Version": "2.17.0",
  "Date": "2023-04-19",
  "Authors@R": "c(\nperson(\"Venkata\",\"Manem\", email = \"mail2mvskumar@gmail.com\",\nrole = c(\"aut\")),\nperson(\"Petr\",\"Smirnov\", email = \"petr.smirnov@uhnresearch.ca\",\nrole = c(\"aut\")),\nperson(\"Ian\",\"Smith\", email = \"ianc.smith@mail.utoronto.ca\",\nrole = c(\"aut\")),\nperson(\"Meghan\",\"Lambie\", email = \"megan.lambie@mail.utoronto.ca\",\nrole = c(\"aut\")),\nperson(\"Christopher\",\"Eeles\", email = \"christopher.eeles@uhnresearch.ca\",\nrole = c(\"aut\")),\nperson(\"Scott\", \"Bratman\", email = \"scott.bratman@rmp.uhn.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": "Computational tool box for radio-genomic analysis which\nintegrates radio-response data, radio-biological modelling and\ncomprehensive cell line annotations for hundreds of cancer cell\nlines. The 'RadioSet' class enables creation and manipulation\nof standardized datasets including information about cancer\ncells lines, radio-response assays and dose-response\nindicators. Included methods allow fitting and plotting\ndose-response data using established radio-biological models\nalong with quality control to validate results. Additional\nfunctions related to fitting and plotting dose response curves,\nquantifying statistical correlation and calculating area under\nthe curve (AUC) or survival fraction (SF) are included. For\nmore details please see the included documentation, references,\nas well as: Manem, V. et al (2018) <doi:10.1101/449793>.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:59 UTC",
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  "Author": "Venkata Manem [aut],\nPetr Smirnov [aut],\nIan Smith [aut],\nMeghan Lambie [aut],\nChristopher Eeles [aut],\nScott Bratman [aut],\nJermiah Joseph [aut],\nBenjamin Haibe-Kains [aut, cre]",
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      "title": "Cleaveland_mut RadioSet subsetted",
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    {
      "page": "availableRSets",
      "title": "Return a table of RadioSets available for download",
      "topics": [
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      ]
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    {
      "page": "checkRSetStructure",
      "title": "A function to verify the structure of a RadioSet",
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    {
      "page": "clevelandSmall",
      "title": "Cleaveland_mut RadioSet subsetted",
      "topics": [
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      "title": "Compute D10",
      "topics": [
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      "title": "Compute SF2",
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      "topics": [
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        "cellInfo,RadioSet-method",
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        "molecularProfilesSlot<-",
        "molecularProfilesSlot<-,RadioSet,list-method",
        "molecularProfilesSlot<-,RadioSet,list_OR_MAE-method",
        "molecularProfilesSlot<-RadioSet,MultiAssayExperiment-method",
        "moleculerProfilesSlot,RadioSet-method",
        "name",
        "name,RadioSet-method",
        "name<-",
        "name<-,RadioSet,character-method",
        "name<-,RadioSet-method",
        "pertNumber",
        "pertNumber,RadioSet-method",
        "pertNumber<-",
        "pertNumber<-,RadioSet,array-method",
        "phenoInfo",
        "phenoInfo,RadioSet,character-method",
        "phenoInfo<-",
        "phenoInfo<-,RadioSet,character,data.frame-method",
        "phenoInfo<-,RadioSet,character,DataFrame-method",
        "radiationInfo",
        "radiationInfo<-",
        "radiationTypes",
        "radiationTypes<-",
        "RadioSet-accessors",
        "sampleInfo",
        "sampleInfo,RadioSet-method",
        "sampleInfo<-",
        "sampleInfo<-,RadioSet,data.frame-method",
        "sampleName,RadioSet-method",
        "sampleNames",
        "sampleNames,RadioSet-method",
        "sampleNames<-",
        "sampleNames<-,RadioSet,character-method",
        "sampleNames<-,RadioSet,list-method",
        "sensitivityInfo,RadioSet,character-method",
        "sensitivityInfo,RadioSet,missing-method",
        "sensitivityInfo,RadioSet-method",
        "sensitivityInfo<-,RadioSet,data.frame-method",
        "sensitivityInfo<-,RadioSet,missing,data.frame-method",
        "sensitivityMeasures,RadioSet-method",
        "sensitivityMeasures<-,RadioSet,character-method",
        "sensitivityProfiles,RadioSet-method",
        "sensitivityProfiles<-,RadioSet,data.frame-method",
        "sensitivityRaw,RadioSet-method",
        "sensitivityRaw<-,RadioSet,array-method",
        "sensitivitySlot",
        "sensitivitySlot<-",
        "sensitvityInfo<-,RadioSet,character,data.frame-method",
        "sensNumber",
        "sensNumber,RadioSet-method",
        "sensNumber<-",
        "sensNumber<-,RadioSet,matrix-method",
        "treamentResponse<-,RadioSet,list-method",
        "treatmentInfo",
        "treatmentInfo,RadioSet-method",
        "treatmentInfo<-",
        "treatmentInfo<-,RadioSet,data.frame-method",
        "treatmentNames",
        "treatmentNames,RadioSet-method",
        "treatmentNames<-",
        "treatmentNames<-,RadioSet,character-method",
        "treatmentResponse",
        "treatmentResponse,RadioSet-method",
        "treatmentResponse<-",
        "treatmentResponse<-,RadioSet,list_OR_LongTable-method",
        "treatmentResponse<-,RadioSet,LongTable-method"
      ]
    },
    {
      "page": "RadioSet-class",
      "title": "A Class to Contain RadioGenomic datasets together with their curations",
      "topics": [
        ".RadioSet",
        "RadioSet-class"
      ]
    },
    {
      "page": "RadioSig",
      "title": "Radiation Signature Class Constructor",
      "topics": [
        "RadioSig"
      ]
    },
    {
      "page": "radSensitivitySig",
      "title": "Creates a signature representing the association between gene expression (or other molecular profile) and radiation dose response, for use in radiation sensitivity analysis.",
      "topics": [
        "radSensitivitySig"
      ]
    },
    {
      "page": "show-RadioSet-method",
      "title": "Show a RadioSet",
      "topics": [
        "show,RadioSet-method"
      ]
    },
    {
      "page": "show-RadioSig-method",
      "title": "Show RadioGx Signatures",
      "topics": [
        "show,RadioSig-method"
      ]
    },
    {
      "page": "showSigAnnot-RadioSig-method",
      "title": "Show the Annotations of a signature object",
      "topics": [
        "showSigAnnot,RadioSig-method"
      ]
    },
    {
      "page": "subsetTo-RadioSet-method",
      "title": "A function to subset a RadioSet to data containing only specified radiations, cells and genes",
      "topics": [
        "subsetTo,RadioSet-method"
      ]
    },
    {
      "page": "summarizeMolecularProfiles-RadioSet-method",
      "title": "Takes molecular data from a RadioSet, and summarises them into one entry per drug",
      "topics": [
        "summarizeMolecularProfiles,RadioSet-method"
      ]
    },
    {
      "page": "summarizeSensitivityProfiles-RadioSet-method",
      "title": "Takes the sensitivity data from a RadioSet, and summarises them into a drug vs cell line table",
      "topics": [
        "summarizeSensitivityProfiles,RadioSet-method"
      ]
    },
    {
      "page": "updateObject-RadioSet-method",
      "title": "Update the RadioSet class after changes in it struture or API",
      "topics": [
        "updateObject,RadioSet-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/RadioGx/raw/HEAD/README.md",
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  ],
  "_vignettes": [
    {
      "source": "RadioGx.Rmd",
      "filename": "RadioGx.html",
      "title": "RadioGx: An R Package for Analysis of Large Radiogenomic Datasets",
      "author": "Venkata Manem, Petr Smirnov, Ian Smith, Meghan Lambie, Christopher Eeles, Scott Bratman, Benjamin Haibe-Kains",
      "engine": "knitr::knitr",
      "headings": [
        "Introduction",
        "Creating a RadioSet",
        "Basic Functionalities of RadioGx",
        "Installing RadioGx",
        "RadioSet",
        "Accessing Data",
        "Accessing metadata",
        "Accessing molecular data",
        "Accessing response data",
        "Fitting Linear Quadratic (LQ) Models",
        "Calculating Dose-Response Metrics",
        "Dose-Response Curves",
        "Summarizing Sensitivity",
        "Summarizing Molecular Data",
        "Molecular Signatures for Biomarker Discovery"
      ],
      "created": "2020-03-31 22:04:43",
      "modified": "2022-07-18 19:01:52",
      "commits": 11
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  "_score": 4.380211241711606,
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  "_nocasepkg": "radiogx",
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