{
  "_id": "6ad4904adc7ca4d810c6d3f2",
  "Package": "doppelgangR",
  "Title": "Identify likely duplicate samples from genomic or meta-data",
  "Version": "1.41.2",
  "Authors@R": "c(person(\"Levi\", \"Waldron\", email = \"lwaldron.research@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Markus\", \"Reister\", email = \"markus.riester@novartis.com\",\nrole = c(\"aut\", \"ctb\")),\nperson(\"Marcel\", \"Ramos\", email = \"marcel.ramos@sph.cuny.edu\",\nrole = \"ctb\"))",
  "Description": "The main function is doppelgangR(), which takes as minimal\ninput a list of ExpressionSet object, and searches all list\npairs for duplicated samples.  The search is based on the\ngenomic data (exprs(eset)), phenotype/clinical data\n(pData(eset)), and \"smoking guns\" - supposedly unique\nidentifiers found in pData(eset).",
  "biocViews": "ImmunoOncology, RNASeq, Microarray, GeneExpression,\nQualityControl",
  "License": "GPL (>=2.0)",
  "Encoding": "UTF-8",
  "URL": "https://github.com/lwaldron/doppelgangR,\nhttps://waldronlab.github.io/doppelgangR",
  "BugReports": "https://github.com/lwaldron/doppelgangR/issues",
  "VignetteBuilder": "knitr",
  "Date": "2025-05-12",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-07-20 14:32:56 UTC",
  "RemoteUrl": "https://github.com/bioc/doppelgangR",
  "RemoteRef": "HEAD",
  "RemoteSha": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-18 09:03:33 UTC",
    "User": "root"
  },
  "Author": "Levi Waldron [aut, cre],\nMarkus Reister [aut, ctb],\nMarcel Ramos [ctb]",
  "Maintainer": "Levi Waldron <lwaldron.research@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "doppelgangR_1.41.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/7dad774a087c44ff4b2b1b71781cfe4bd409ff6ab8edcbd21db946336fd4a1db",
  "_filesize": 414349,
  "_sha256": "7dad774a087c44ff4b2b1b71781cfe4bd409ff6ab8edcbd21db946336fd4a1db",
  "_expires": "2027-01-26T09:24:24.000Z",
  "_created": "2026-10-18T09:03:33.000Z",
  "_published": "2026-10-18T09:24:26.621Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 10
  },
  "_upstream": "https://github.com/bioc/doppelgangR",
  "_commit": {
    "id": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
    "author": "Levi Waldron <lwaldron.research@gmail.com>",
    "committer": "Levi Waldron <lwaldron.research@gmail.com>",
    "message": "bump version\n",
    "time": 1784557976
  },
  "_maintainer": {
    "name": "Levi Waldron",
    "email": "lwaldron.research@gmail.com",
    "login": "lwaldron",
    "twitter": "@LeviWaldron1",
    "description": "I teach biostatistics, develop for Bioconductor, and have an active research program in cancer genomics and in metagenomic profiling of the human microbiome.",
    "uuid": 639942
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 117635588627,
      "time": 155,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12131458094"
    },
    {
      "job": 117635588660,
      "time": 565,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12131676954"
    },
    {
      "job": 117635588598,
      "time": 590,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12131972321"
    },
    {
      "job": 117635588574,
      "time": 400,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12131976763"
    },
    {
      "job": 117635588664,
      "time": 406,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12131592899"
    },
    {
      "job": 117634527519,
      "time": 315,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12131097656"
    },
    {
      "job": 117635588635,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12131169034"
    },
    {
      "job": 117635588625,
      "time": 1189,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12130979915"
    },
    {
      "job": 117635588665,
      "time": 1023,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12132156247"
    },
    {
      "job": 117635588596,
      "time": 1126,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12131433393"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "impute",
      "role": "Imports"
    },
    {
      "package": "digest",
      "role": "Imports"
    },
    {
      "package": "mnormt",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "curatedOvarianData",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "S4Vectors",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-43",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-47",
      "n": 7
    },
    {
      "week": "2026-18",
      "n": 4
    },
    {
      "week": "2026-20",
      "n": 1
    },
    {
      "week": "2026-29",
      "n": 6
    },
    {
      "week": "2026-30",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.2",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "immunooncology",
    "rnaseq",
    "microarray",
    "geneexpression",
    "qualitycontrol",
    "bioconductor-package",
    "u24ca289073"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "lwaldron",
      "count": 123,
      "uuid": 639942
    },
    {
      "user": "link-ny",
      "count": 47,
      "uuid": 4392950
    },
    {
      "user": "lima1",
      "count": 26,
      "uuid": 364466
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "dtenenba",
      "count": 4,
      "uuid": 2286826
    },
    {
      "user": "maddahi93",
      "count": 3,
      "uuid": 10553448
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 478,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 616,
    "source": "https://www.bioconductor.org/packages/stats/bioc/doppelgangR"
  },
  "_mentions": 3,
  "_devurl": "https://github.com/lwaldron/doppelgangr",
  "_pkgdown": "https://waldronlab.github.io/doppelgangR",
  "_searchresults": 50,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/doppelgangR.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/waldronlab/doppelgangr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "colFinder",
    "corFinder",
    "doppelgangR",
    "dst",
    "mst.mle",
    "outlierFinder",
    "phenoDist",
    "phenoFinder",
    "plot",
    "print",
    "pst",
    "qst",
    "rst",
    "show",
    "smokingGunFinder",
    "st.mle",
    "summary",
    "vectorHammingDist",
    "vectorWeightedDist"
  ],
  "_help": [
    {
      "page": "doppelgangR-package",
      "title": "Identify likely duplicate samples from genomic or meta-data",
      "topics": [
        "doppelgangR-package"
      ]
    },
    {
      "page": "colFinder",
      "title": "Calculate pairwise similarities of colData between samples for a list containing two DataFrame",
      "topics": [
        "colFinder"
      ]
    },
    {
      "page": "corFinder",
      "title": "Calculate pair-wise correlations between samples using the expr() slots of a list of two ExpressionSets.",
      "topics": [
        "corFinder"
      ]
    },
    {
      "page": "DoppelGang-class",
      "title": "DoppelGang S4 class",
      "topics": [
        "DoppelGang",
        "DoppelGang-class",
        "print,DoppelGang-method",
        "show,DoppelGang-method",
        "summary,DoppelGang-method"
      ]
    },
    {
      "page": "doppelgangR",
      "title": "doppelgangR",
      "topics": [
        "doppelgangR"
      ]
    },
    {
      "page": "dst",
      "title": "Skew-t Distribution",
      "topics": [
        "dst",
        "pst",
        "qst",
        "rst"
      ]
    },
    {
      "page": "mst.mle",
      "title": "Maximum likelihood estimation for a (multivariate) skew-t distribution",
      "topics": [
        "mst.mle",
        "st.mle"
      ]
    },
    {
      "page": "outlierFinder",
      "title": "Identifies outliers in a similarity matrix.",
      "topics": [
        "outlierFinder"
      ]
    },
    {
      "page": "phenoDist",
      "title": "Calculate distance between two vectors, rows of one matrix/dataframe, or rows of two matrices/dataframes.",
      "topics": [
        "phenoDist"
      ]
    },
    {
      "page": "phenoFinder",
      "title": "Calculate pairwise similarities of phenoData between samples for a list containing two ExpressionSets",
      "topics": [
        "phenoFinder"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Histograms of all pairwise sample correlations, showing identified doppelgangers.",
      "topics": [
        "plot,DoppelGang",
        "plot,DoppelGang,ANY-method",
        "plot,DoppelGang-method",
        "plot-methods",
        "plot.DoppelGang",
        "plot.doppelgangR"
      ]
    },
    {
      "page": "smokingGunFinder",
      "title": "Find doppelgangers based on \"smoking gun\" phenotypes - those that should be unique to each patient.",
      "topics": [
        "smokingGunFinder"
      ]
    },
    {
      "page": "vectorHammingDist",
      "title": "Calculate Hamming Distance between two vectors, using pairwise complete observations.",
      "topics": [
        "vectorHammingDist"
      ]
    },
    {
      "page": "vectorWeightedDist",
      "title": "Calculate a weighted distance between two vectors, using pairwise complete observations.",
      "topics": [
        "vectorWeightedDist"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/doppelgangR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "digest",
    "edgeR",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "genefilter",
    "generics",
    "GenomicRanges",
    "globals",
    "glue",
    "httr",
    "impute",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "listenv",
    "locfit",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "mnormt",
    "nlme",
    "openssl",
    "parallelly",
    "pkgconfig",
    "png",
    "R6",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "survival",
    "sva",
    "sys",
    "vctrs",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "doppelgangR.Rmd",
      "filename": "doppelgangR.html",
      "title": "doppelgängR",
      "author": "Levi Waldron",
      "engine": "knitr::rmarkdown",
      "headings": [
        "doppelgängR",
        "Introduction",
        "Data types",
        "Case Study: Batch correction in Japanese datasets",
        "Important options",
        "Changing sensitivity",
        "Use of the ExpressionSet",
        "Parallelizing",
        "Caching",
        "Session Info"
      ],
      "created": "2016-03-17 00:22:39",
      "modified": "2026-07-17 21:32:40",
      "commits": 9
    }
  ],
  "_score": 7.373371817181301,
  "_indexed": true,
  "_nocasepkg": "doppelgangr",
  "_universes": [
    "bioc",
    "lwaldron"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.2",
      "date": "2026-10-18T09:08:52.000Z",
      "distro": "resolute",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/e51373cf0ca482127b91f0ab3ae2f2032cc796e1e15849181151594038c5f435",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.2",
      "date": "2026-10-18T09:09:14.000Z",
      "distro": "resolute",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/8390ebbe9f99c85824a2a48578c934f1b27757c051caea5abf3940bdae25766b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.2",
      "date": "2026-10-18T09:06:06.000Z",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/a6b0819047e3ec7e99185c303896c5e19c19c41824f9a80e6e8ce7cfcc8000f5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.2",
      "date": "2026-10-18T09:05:36.000Z",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/4d4f992e5a39f377cedf4997831f878aafa2606661c9771836c1bed9c5223470",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.2",
      "date": "2026-10-18T09:06:28.000Z",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/e90ed599bf9f62a94dbd9d8d60ed797dbf612cc382a5a42aabf5aca2eb3012ab",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.2",
      "date": "2026-10-18T09:17:48.000Z",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/0c39f3d23a85a1064787c91705a867af347bcc94af766258b5a5c53131e03251",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.2",
      "date": "2026-10-18T09:16:09.000Z",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/86f7c06b9babe5294f6fbd325d3dc05ebd58c83aeccaa8f998e7a034f433bad8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.2",
      "date": "2026-10-18T09:17:56.000Z",
      "commit": "bb6121dbc9bd37d36c52a31680fe520a8508b102",
      "fileid": "https://r2.ropensci.org/a281945f30bab042672030063c5fb8f85f0d37dbb33dfc07fe2c49d7c70ff8c0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39113517803"
    }
  ]
}