{
  "_id": "6aabc2cc3d719c1f8406e66b",
  "Package": "oppar",
  "Type": "Package",
  "Title": "Outlier profile and pathway analysis in R",
  "Version": "1.41.0",
  "Date": "2016",
  "Authors@R": "c(\nperson(\"Chenwei\", \"Wang\", email = \"chenwei.wang@qut.edu.au\", role = \"aut\"),\nperson(\"Alperen\", \"Taciroglu\", role = \"aut\"),\nperson(\"Stefan R\", \"Maetschke\", role = \"aut\"),\nperson(\"Colleen C\", \"Nelson\", role = \"aut\"),\nperson(\"Mark\", \"Ragan\", role = \"aut\"),\nperson(\"Melissa\", \"Davis\", email = \"davis.m@wehi.edu.au\", role = \"aut\"),\nperson(\"Soroor\", \"Hediyeh zadeh\", email = \"hediyehzadeh.s@wehi.edu.au\",role = \"cre\"),\nperson(\"Momeneh\",\"Foroutan\", email= \"mforoutan@student.unimelb.edu.au\", role = \"ctr\"))",
  "Description": "The R implementation of mCOPA package published by Wang et\nal. (2012). Oppar provides methods for Cancer Outlier profile\nAnalysis. Although initially developed to detect outlier genes\nin cancer studies, methods presented in oppar can be used for\noutlier profile analysis in general. In addition, tools are\nprovided for gene set enrichment and pathway analysis.",
  "biocViews": "Pathways, GeneSetEnrichment, SystemsBiology, GeneExpression,\nSoftware",
  "License": "GPL-2",
  "LazyData": "true",
  "Collate": "'class_OPPARList.R' 'class_nuchar.R' 'getSampleOutlier.R'\n'getSubtypeProbes.R' 'gsva.R' 'opa-generic-methods.R' 'oppar.R'\n'utils.R' 'zzz.R'",
  "RoxygenNote": "5.0.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev libpng-dev\nlibxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:19 UTC",
  "RemoteUrl": "https://github.com/bioc/oppar",
  "RemoteRef": "HEAD",
  "RemoteSha": "892e38d188fe3ce5531183b48c5559e654205f11",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-17 09:37:17 UTC",
    "User": "root"
  },
  "Author": "Chenwei Wang [aut],\nAlperen Taciroglu [aut],\nStefan R Maetschke [aut],\nColleen C Nelson [aut],\nMark Ragan [aut],\nMelissa Davis [aut],\nSoroor Hediyeh zadeh [cre],\nMomeneh Foroutan [ctr]",
  "Maintainer": "Soroor Hediyeh zadeh <hediyehzadeh.s@wehi.edu.au>",
  "_user": "bioc",
  "_type": "src",
  "_file": "oppar_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b115051392b90395d37e0ebf65b9aeea039b4878842b9fd0c846af038fcb4bbe",
  "_filesize": 3699454,
  "_sha256": "b115051392b90395d37e0ebf65b9aeea039b4878842b9fd0c846af038fcb4bbe",
  "_expires": "2026-12-26T10:36:58.000Z",
  "_created": "2026-09-17T09:37:17.000Z",
  "_published": "2026-09-17T10:37:00.534Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 14
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289",
  "_status": "success",
  "_upstream": "https://github.com/bioc/oppar",
  "_commit": {
    "id": "892e38d188fe3ce5531183b48c5559e654205f11",
    "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": 1777380199
  },
  "_maintainer": {
    "name": "Soroor Hediyeh zadeh",
    "email": "hediyehzadeh.s@wehi.edu.au",
    "login": "soroorh",
    "description": "",
    "uuid": 7257233
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 105152439334,
      "time": 214,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10490132743"
    },
    {
      "job": 105152439430,
      "time": 348,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10489299438"
    },
    {
      "job": 105152439534,
      "time": 455,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10489649037"
    },
    {
      "job": 105152439491,
      "time": 338,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10490396839"
    },
    {
      "job": 105152439494,
      "time": 405,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10489354432"
    },
    {
      "job": 105152439414,
      "time": 228,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10492131594"
    },
    {
      "job": 105152439444,
      "time": 495,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10489359763"
    },
    {
      "job": 105152439439,
      "time": 270,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10491703436"
    },
    {
      "job": 105152439487,
      "time": 689,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10489609691"
    },
    {
      "job": 105150682229,
      "time": 348,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10490291388"
    },
    {
      "job": 105152439465,
      "time": 212,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10489383877"
    },
    {
      "job": 105152439480,
      "time": 421,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10489464210"
    },
    {
      "job": 105152439703,
      "time": 412,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "10489929217"
    },
    {
      "job": 105152439837,
      "time": 319,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "10489329342"
    },
    {
      "job": 105152439725,
      "time": 409,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10489993944"
    },
    {
      "job": 105152439772,
      "time": 328,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "10489443919"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "GSEABase",
      "role": "Imports"
    },
    {
      "package": "GSVA",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "GO.db",
      "role": "Suggests"
    },
    {
      "package": "snow",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "pathways",
    "genesetenrichment",
    "systemsbiology",
    "geneexpression",
    "software"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 467,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 609,
    "source": "https://www.bioconductor.org/packages/stats/bioc/oppar"
  },
  "_searchresults": 8,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/oppar.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "getSampleOutlier",
    "getSubtypeProbes",
    "gsva",
    "opa",
    "show"
  ],
  "_datasets": [
    {
      "name": "bcm",
      "title": "Breast cancer metastases from different anatomical sites",
      "object": "GSE46141",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "eset",
      "title": "Tomlins et al. Prostate Cancer data (GEO: GSE6099)",
      "object": "tomlins",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "maupin",
      "title": "Maupin's TGFb data and a TGFb gene signature",
      "object": "Maupin",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bcm",
      "title": "Breast cancer metastases from different anatomical sites",
      "topics": [
        "bcm"
      ]
    },
    {
      "page": "eset",
      "title": "Tomlins et al. Prostate Cancer data (GEO: GSE6099)",
      "topics": [
        "eset"
      ]
    },
    {
      "page": "getSampleOutlier",
      "title": "Retrieving outlier genes in samples",
      "topics": [
        "getSampleOutlier",
        "getSampleOutlier,matrix,nuchar-method",
        "getSampleOutlier,OPPARList,nuchar-method"
      ]
    },
    {
      "page": "getSubtypeProbes",
      "title": "Retrieving outlier genes from a group of related samples",
      "topics": [
        "getSubtypeProbes",
        "getSubtypeProbes,matrix,nuchar-method",
        "getSubtypeProbes,OPPARList,nuchar-method"
      ]
    },
    {
      "page": "gsva",
      "title": "gsva",
      "topics": [
        "gsva",
        "gsva,ExpressionSet,GeneSetCollection-method",
        "gsva,ExpressionSet,list-method",
        "gsva,matrix,GeneSetCollection-method",
        "gsva,matrix,list-method"
      ]
    },
    {
      "page": "maupin",
      "title": "Maupin's TGFb data and a TGFb gene signature",
      "topics": [
        "maupin"
      ]
    },
    {
      "page": "opa",
      "title": "Outlier profile Analysis",
      "topics": [
        "opa",
        "opa,ExpressionSet-method",
        "opa,matrix-method"
      ]
    },
    {
      "page": "oppar",
      "title": "oppar: A package for outlier profile and pathway analysis.",
      "topics": [
        "oppar-package",
        "oppar"
      ]
    },
    {
      "page": "OPPARList-class",
      "title": "A S4 class for the output of OPPAR main function, opa.",
      "topics": [
        "$,OPPARList-method",
        "OPPARList-class",
        "show,OPPARList-method"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "assorthead",
    "beachmat",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "biocmake",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "DelayedMatrixStats",
    "dir.expiry",
    "dplyr",
    "fastmap",
    "filelock",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "glue",
    "graph",
    "GSEABase",
    "GSVA",
    "h5mread",
    "HDF5Array",
    "httr",
    "httr2",
    "IRanges",
    "irlba",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "memuse",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "png",
    "purrr",
    "R6",
    "Rcpp",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "rjson",
    "rlang",
    "RSQLite",
    "rsvd",
    "S4Arrays",
    "S4Vectors",
    "ScaledMatrix",
    "Seqinfo",
    "SingleCellExperiment",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "oppar.Rmd",
      "filename": "oppar.html",
      "title": "OPPAR: Outlier Profile and Pathway Analysis in R",
      "author": "Soroor Hediyehzadeh",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Analysis of Tomlins et al. prostate cancer dataset",
        "Gene Set Enrichment Analysis"
      ],
      "created": "2016-04-06 16:10:37",
      "modified": "2018-09-06 15:52:20",
      "commits": 2
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "oppar",
  "_universes": [
    "bioc",
    "soroorh"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-09-17T09:40:55.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/12caf6166c5e066f007ec0c2b7bd761825491c28740cdc634395a335e2a69b23",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-09-17T09:41:50.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/3c42b39bc8b888caaf2874f0c9e10492ce6b28fe638b3ce2c05e4d370262cc9a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-09-17T09:40:57.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/419212f4afb7794ff7f1e26f705d20dfc765a682c74be7c1f00145a753e46a2f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-09-17T09:41:35.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/5d3517afc165488f5edf1a1cc9526db5d042e50d5483e88daf6b200916a45329",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-09-17T10:33:30.000Z",
      "arch": "aarch64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/0186abc7c6fc9bf0d9cc17f0026a437d73654ce937bfec5c4cf06b9e54983199",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-09-17T09:42:21.000Z",
      "arch": "x86_64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/da571c365085b9a8a0d5e4a20292777517a66c7a0c6543efa940b1496573cb0a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-09-17T10:33:34.000Z",
      "arch": "aarch64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/3d7c8610839eda523d039d3d9505c728162ac835371c84256c7ff86f7ba45900",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-09-17T09:44:12.000Z",
      "arch": "x86_64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/da5e04eebf2bade03db7b4c89a02c3201cde5c98f6ca620edf99a28ba964003c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-09-17T09:41:32.000Z",
      "arch": "emscripten",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/d2f8edea5d92fc59538e55f82bde84f5c60959b8d3b814c440f25933fff9fd96",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-09-17T09:41:24.000Z",
      "arch": "aarch64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/e561034e1a3b406891cbba585e585a186ba9485fc00ad2baecfa61f9601c9f39",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-09-17T09:39:55.000Z",
      "arch": "x86_64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/b4ffe8b3ee36ed62553679980c61cab4c576d49eefe1ef82f33cf7704f66879c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-09-17T09:40:31.000Z",
      "arch": "x86_64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/a01a75324770ad08f4a99d9fd737f12c19f008da57035e0c3742b78ca9b9fdb1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-09-17T09:41:37.000Z",
      "arch": "aarch64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/d71968c1fe4f762f6f1a757d2a23122fb7f621bc36d912b5198f36de0f9e15c2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-09-17T09:39:38.000Z",
      "arch": "x86_64",
      "commit": "892e38d188fe3ce5531183b48c5559e654205f11",
      "fileid": "https://r2.ropensci.org/1c783b68712c849ccf178d9735754d235c6126dd6de762fcb7876440709c9b22",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/35205628289"
    }
  ]
}