{
  "_id": "6a142a56acfb0bcc41d40863",
  "Package": "Xeva",
  "Type": "Package",
  "Title": "Analysis of patient-derived xenograft (PDX) data",
  "Version": "1.29.0",
  "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",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "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.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:40 UTC",
  "RemoteUrl": "https://github.com/bioc/Xeva",
  "RemoteRef": "HEAD",
  "RemoteSha": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-25 10:46:06 UTC",
    "User": "root"
  },
  "Author": "Arvind Mer [aut],\nBenjamin Haibe-Kains [aut, cre]",
  "MD5sum": "e2ecd3bf167c67902f88ff6417481fba",
  "_user": "bioc",
  "_type": "src",
  "_file": "Xeva_1.29.0.tar.gz",
  "_fileid": "efc29a2844e51c926854248c312f00ad602017112a5e9c9292fed6169b2b6736",
  "_filesize": 1814476,
  "_sha256": "efc29a2844e51c926854248c312f00ad602017112a5e9c9292fed6169b2b6736",
  "_created": "2026-05-25T10:46:06.000Z",
  "_published": "2026-05-25T10:54:14.044Z",
  "_jobs": [
    {
      "job": 77698550056,
      "time": 206,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7196731532"
    },
    {
      "job": 77698550108,
      "time": 424,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7196784211"
    },
    {
      "job": 77698550066,
      "time": 365,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7196770328"
    },
    {
      "job": 77698550060,
      "time": 243,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7196740902"
    },
    {
      "job": 77698550088,
      "time": 224,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7196736184"
    },
    {
      "job": 77697770527,
      "time": 365,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196678395"
    },
    {
      "job": 77698550059,
      "time": 170,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196722208"
    },
    {
      "job": 77698550148,
      "time": 306,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7196755993"
    },
    {
      "job": 77698550126,
      "time": 345,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7196764966"
    },
    {
      "job": 77698550091,
      "time": 335,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7196762865"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Xeva",
  "_commit": {
    "id": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380580
  },
  "_maintainer": {
    "name": "Benjamin Haibe-Kains",
    "email": "benjamin.haibe.kains@utoronto.ca",
    "login": "bhaibeka",
    "description": "",
    "uuid": 594954
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BBmisc",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "Rmisc",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "nlme",
      "role": "Imports"
    },
    {
      "package": "PharmacoGx",
      "role": "Imports"
    },
    {
      "package": "downloader",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "geneexpression",
    "pharmacogenetics",
    "pharmacogenomics",
    "software",
    "classification"
  ],
  "_stars": 11,
  "_contributors": [
    {
      "user": "spocks",
      "count": 342,
      "uuid": 5002382
    },
    {
      "user": "bhaibeka",
      "count": 15,
      "uuid": 594954
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "gangeshberi",
      "count": 14,
      "uuid": 41119826
    },
    {
      "user": "benmbrew",
      "count": 11,
      "uuid": 8471353
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "jenliketen",
      "count": 8,
      "uuid": 41165820
    },
    {
      "user": "elijahxtai",
      "count": 2,
      "uuid": 5567908
    },
    {
      "user": "guanqiaofeng",
      "count": 1,
      "uuid": 42392742
    },
    {
      "user": "jjjermiah",
      "count": 1,
      "uuid": 44614774
    },
    {
      "user": "sisiranair",
      "count": 1,
      "uuid": 41380598
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 344,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Xeva"
  },
  "_devurl": "https://github.com/bhklab/xeva",
  "_searchresults": 35,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Xeva.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bhklab/xeva",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "ABC",
    "addExperimentalDesign",
    "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"
  ],
  "_datasets": [
    {
      "name": "brca",
      "title": "PDXE breast cancer dataset",
      "object": "brca",
      "file": "brca.rda",
      "class": [
        "XevaSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "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
    }
  ],
  "_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"
      ]
    },
    {
      "page": "slope",
      "title": "Computes slope",
      "topics": [
        "slope"
      ]
    },
    {
      "page": "subsetXeva",
      "title": "Subset Xeva object.",
      "topics": [
        "subsetXeva"
      ]
    },
    {
      "page": "summarizeMolecularProfiles",
      "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"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Xeva/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "base64enc",
    "BBmisc",
    "bench",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocParallel",
    "bitops",
    "boot",
    "bslib",
    "BumpyMatrix",
    "cachem",
    "caTools",
    "celestial",
    "checkmate",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "commonmark",
    "ComplexHeatmap",
    "coop",
    "CoreGx",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "data.table",
    "DelayedArray",
    "digest",
    "doParallel",
    "downloader",
    "dplyr",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fastmatch",
    "fgsea",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "GlobalOptions",
    "glue",
    "gplots",
    "gtable",
    "gtools",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "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",
    "nlme",
    "otel",
    "PharmacoGx",
    "piano",
    "pillar",
    "pkgconfig",
    "plotrix",
    "plyr",
    "png",
    "pracma",
    "profmem",
    "promises",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "relations",
    "reshape2",
    "rjson",
    "rlang",
    "rmarkdown",
    "Rmisc",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "sets",
    "shape",
    "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"
  ],
  "_vignettes": [
    {
      "source": "Xeva.Rnw",
      "filename": "Xeva.pdf",
      "title": "The Xeva User's Guide",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2019-03-06 20:51:56",
      "modified": "2023-04-19 00:23:24",
      "commits": 6
    }
  ],
  "_score": 6.585460729508501,
  "_indexed": true,
  "_nocasepkg": "xeva",
  "_universes": [
    "bioc",
    "bhaibeka",
    "bhklab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-25T10:50:34.000Z",
      "distro": "noble",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "c633c88f29ab8428bea0b3b9f5c1a2f82a04b34b5a5009759890f960d951cefa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-25T10:49:41.000Z",
      "distro": "noble",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "21e19646cfa54545bcffc3eac10e5141599734d3467c426437efdb0be1a853dc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-25T10:48:36.000Z",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "1611d3b66d1952d7fcdeda9791180fd50bdba706df871694652f61e6af631bc2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-25T10:48:18.000Z",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "fe3198f884a329215b7df1c9f57d42ac0c139a52a13bae18610dac107f1745ee",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.29.0",
      "date": "2026-05-25T10:49:38.000Z",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "b877a98a5ad9047ff35fcd5eb8ba5fa555aaf998b1521741cb504f087717c68f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-25T10:48:23.000Z",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "3282aea6fc2c2538127e6bbfb6f1ed1e5d9b0ed3709c5377089382868c203a16",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-25T10:49:11.000Z",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "6a278eab765f960bea8e6077fab9d773f1ccc003716c3dfa896eabf10f78d101",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-25T10:49:06.000Z",
      "commit": "c252c0c2bf29e64ca14b3c895d09247f601b8666",
      "fileid": "0659cc1dfa7ef09d4088e8b6bbaa8023662c55239e45b3477d9c0dc0605c91be",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396322434"
    }
  ]
}