{
  "_id": "6a1b08711d7bb097a0a0503f",
  "Package": "Xeva",
  "Type": "Package",
  "Title": "Analysis of patient-derived xenograft (PDX) data",
  "Version": "1.28.0",
  "Date": "2025-03-20",
  "Authors@R": "c(\nperson(given=\"Arvind\", family=\"Mer\", role = c(\"aut\")),\nperson(\"Benjamin\", \"Haibe-Kains\",\nemail = \"benjamin.haibe.kains@utoronto.ca\", role = c(\"aut\", \"cre\"))\n)",
  "Maintainer": "Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>",
  "Description": "The Xeva package provides efficient and powerful functions\nfor patient-drived xenograft (PDX) based pharmacogenomic data\nanalysis. This package contains a set of functions to perform\nanalysis of patient-derived xenograft data. This package was\ndeveloped by the BHKLab, for further information please see our\ndocumentation.",
  "License": "GPL-3",
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  "biocViews": "GeneExpression, Pharmacogenetics, Pharmacogenomics,\nSoftware, Classification",
  "BugReports": "https://github.com/bhklab/Xeva/issues",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev perl zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:40 UTC",
  "RemoteUrl": "https://github.com/bioc/Xeva",
  "RemoteRef": "RELEASE_3_23",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "Author": "Arvind Mer [aut],\nBenjamin Haibe-Kains [aut, cre]",
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    "source": "https://www.bioconductor.org/packages/stats/bioc/Xeva"
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  "_devurl": "https://github.com/bhklab/xeva",
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  "_assets": [
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  "_realowner": "bioc",
  "_cranurl": false,
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    "angle",
    "AUC",
    "batchInfo",
    "createXevaSet",
    "dosePlot",
    "downloadXevaSet",
    "drugInform",
    "drugSensitivitySig",
    "getExperiment",
    "getMolecularProfiles",
    "lmm",
    "modelInfo",
    "mRECIST",
    "plotBatch",
    "plotmRECIST",
    "plotPDX",
    "response",
    "selectModelIds",
    "sensitivity",
    "setResponse",
    "slope",
    "subsetXeva",
    "summarizeMolecularProfiles",
    "summarizeResponse",
    "TGI",
    "waterfall"
  ],
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      "name": "brca",
      "title": "PDXE breast cancer dataset",
      "object": "brca",
      "file": "brca.rda",
      "class": [
        "XevaSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "PDXMI",
      "title": "PDX-MI data",
      "object": "PDXMI",
      "file": "PDXMI.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Module",
        "Field",
        "Recommendation",
        "id"
      ],
      "rows": 45,
      "table": true,
      "tojson": true
    },
    {
      "name": "repdx",
      "title": "Example PDX dataset",
      "object": "repdx",
      "file": "repdx.rda",
      "class": [
        "XevaSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  ],
  "_help": [
    {
      "page": "ABC",
      "title": "area between curves Computes the area between two time-volume curves.",
      "topics": [
        "ABC"
      ]
    },
    {
      "page": "addExperimentalDesign",
      "title": "Add a new experimental design",
      "topics": [
        "addExperimentalDesign",
        "addExperimentalDesign,XevaSet-method"
      ]
    },
    {
      "page": "angle",
      "title": "compute angle Computes the angle between two time-volume curves.",
      "topics": [
        "angle"
      ]
    },
    {
      "page": "AUC",
      "title": "area under the curve 'AUC' Returns area under the curve",
      "topics": [
        "AUC"
      ]
    },
    {
      "page": "batchInfo",
      "title": "Get batch information",
      "topics": [
        "batchInfo",
        "batchInfo,XevaSet-method"
      ]
    },
    {
      "page": "brca",
      "title": "PDXE breast cancer dataset",
      "topics": [
        "brca"
      ]
    },
    {
      "page": "createXevaSet",
      "title": "XevaSet constructor",
      "topics": [
        "createXevaSet"
      ]
    },
    {
      "page": "dosePlot",
      "title": "plot dose data",
      "topics": [
        "dosePlot"
      ]
    },
    {
      "page": "downloadXevaSet",
      "title": "Download a XevaSet object or table of available XevaSet objects",
      "topics": [
        "downloadXevaSet"
      ]
    },
    {
      "page": "drugInform",
      "title": "Get drug information Get the drug information slot from a XevaSet object.",
      "topics": [
        "drugInform",
        "drugInform,XevaSet-method"
      ]
    },
    {
      "page": "drugSensitivitySig",
      "title": "get drug sensitivity values",
      "topics": [
        "drugSensitivitySig"
      ]
    },
    {
      "page": "getExperiment",
      "title": "Get PDX experiment data",
      "topics": [
        "getExperiment",
        "getExperiment,XevaSet-method"
      ]
    },
    {
      "page": "getMolecularProfiles",
      "title": "Get molecular profiles from a XevaSet object",
      "topics": [
        "getMolecularProfiles"
      ]
    },
    {
      "page": "lmm",
      "title": "linear mixed model",
      "topics": [
        "lmm"
      ]
    },
    {
      "page": "modelInfo",
      "title": "modelInfo Generic Generic for modelInfo method",
      "topics": [
        "modelInfo",
        "modelInfo,XevaSet-method"
      ]
    },
    {
      "page": "mRECIST",
      "title": "Computes the mRECIST",
      "topics": [
        "mRECIST"
      ]
    },
    {
      "page": "PDXMI",
      "title": "PDX-MI data",
      "topics": [
        "PDXMI"
      ]
    },
    {
      "page": "plotmRECIST",
      "title": "To plot mRECIST values",
      "topics": [
        "plotmRECIST"
      ]
    },
    {
      "page": "plotPDX",
      "title": "Plot batch data",
      "topics": [
        "plotBatch",
        "plotPDX"
      ]
    },
    {
      "page": "print.batchResponse",
      "title": "Print the batch response",
      "topics": [
        "print.batchResponse"
      ]
    },
    {
      "page": "print.modelResponse",
      "title": "Print the model response",
      "topics": [
        "print.modelResponse"
      ]
    },
    {
      "page": "print.pdxBatch",
      "title": "Print the pdx batch",
      "topics": [
        "print.pdxBatch"
      ]
    },
    {
      "page": "repdx",
      "title": "Example PDX dataset",
      "topics": [
        "repdx"
      ]
    },
    {
      "page": "response",
      "title": "compute PDX response",
      "topics": [
        "response"
      ]
    },
    {
      "page": "selectModelIds",
      "title": "To select model IDs based on drug name and/or tissue type.",
      "topics": [
        "selectModelIds",
        "selectModelIds,XevaSet-method"
      ]
    },
    {
      "page": "sensitivity",
      "title": "Get sensitivity for an Xeva object",
      "topics": [
        "sensitivity"
      ]
    },
    {
      "page": "setResponse",
      "title": "set PDX response",
      "topics": [
        "setResponse"
      ]
    },
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      "page": "slope",
      "title": "Computes slope",
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        "slope"
      ]
    },
    {
      "page": "subsetXeva",
      "title": "Subset Xeva object.",
      "topics": [
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      ]
    },
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      "title": "Summarize molecular profiles",
      "topics": [
        "summarizeMolecularProfiles"
      ]
    },
    {
      "page": "summarizeResponse",
      "title": "Summarize Response of PDXs",
      "topics": [
        "summarizeResponse"
      ]
    },
    {
      "page": "TGI",
      "title": "tumor growth inhibition (TGI) Computes the tumor growth inhibition (TGI) between two time-volume curves",
      "topics": [
        "TGI"
      ]
    },
    {
      "page": "waterfall",
      "title": "waterfall plot Creates waterfall plot for a given drug.",
      "topics": [
        "waterfall"
      ]
    }
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