{
  "_id": "6a266c10794753ddbc3e83bf",
  "Package": "decontam",
  "Type": "Package",
  "Title": "Identify Contaminants in Marker-gene and Metagenomics Sequencing\nData",
  "Version": "1.32.0",
  "Date": "2021-02-19",
  "Authors@R": "c(person(given = \"Benjamin\", family = \"Callahan\", role = c(\"aut\",\"cre\"),\nemail = \"benjamin.j.callahan@gmail.com\"),\nperson(given = \"Nicole Marie\", family = \"Davis\", role = \"aut\"),\nperson(given = \"Felix G.M.\", family = \"Ernst\", role = \"ctb\",\nemail = \"felix.gm.ernst@outlook.com\",\ncomment = c(ORCID = \"0000-0001-5064-0928\")))",
  "Maintainer": "Benjamin Callahan <benjamin.j.callahan@gmail.com>",
  "Description": "Simple statistical identification of contaminating\nsequence features in marker-gene or metagenomics data. Works on\nany kind of feature derived from environmental sequencing data\n(e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA\nquantitation data or sequenced negative control samples.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, Microbiome, Sequencing, Classification,\nMetagenomics",
  "URL": "https://github.com/benjjneb/decontam",
  "BugReports": "https://github.com/benjjneb/decontam/issues",
  "RoxygenNote": "7.1.1",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:43 UTC",
  "RemoteUrl": "https://github.com/bioc/decontam",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "783a69b26ad74d418fa79b5cf597a68df39f7119",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 07:10:42 UTC",
    "User": "root"
  },
  "Author": "Benjamin Callahan [aut, cre],\nNicole Marie Davis [aut],\nFelix G.M. Ernst [ctb] (ORCID: <https://orcid.org/0000-0001-5064-0928>)",
  "MD5sum": "6bcd1434b1a5dd9f01d805157dfff9db",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "decontam_1.32.0.tar.gz",
  "_fileid": "a53fee0aa425949cbf7689738d2ce17526f4cb588897f5b6a43da03c2a1dd8a6",
  "_filesize": 589164,
  "_sha256": "a53fee0aa425949cbf7689738d2ce17526f4cb588897f5b6a43da03c2a1dd8a6",
  "_created": "2026-06-08T07:10:42.000Z",
  "_published": "2026-06-08T07:15:28.801Z",
  "_jobs": [
    {
      "job": 80040394781,
      "time": 154,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7473671258"
    },
    {
      "job": 80040394830,
      "time": 200,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7473683419"
    },
    {
      "job": 80040394795,
      "time": 205,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473684844"
    },
    {
      "job": 80040394812,
      "time": 125,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7473671227"
    },
    {
      "job": 80040394822,
      "time": 102,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473666489"
    },
    {
      "job": 80039760062,
      "time": 269,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473630010"
    },
    {
      "job": 80040394850,
      "time": 115,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473661192"
    },
    {
      "job": 80040394853,
      "time": 111,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7473660364"
    },
    {
      "job": 80040394840,
      "time": 98,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7473657019"
    },
    {
      "job": 80040394887,
      "time": 112,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7473660466"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/decontam",
  "_commit": {
    "id": "783a69b26ad74d418fa79b5cf597a68df39f7119",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380463
  },
  "_maintainer": {
    "name": "Benjamin Callahan",
    "email": "benjamin.j.callahan@gmail.com",
    "login": "benjjneb",
    "description": "Physics -> Evolution -> Microbiome -> Bioinformatics",
    "uuid": 5797204
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "version": ">= 3.4.1",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.1.0",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "version": ">= 1.4.1",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "phyloseq",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 9,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "microbiome",
    "sequencing",
    "classification",
    "metagenomics",
    "amplicon",
    "bioinformatics",
    "contamination",
    "metabarcoding"
  ],
  "_stars": 171,
  "_contributors": [
    {
      "user": "benjjneb",
      "count": 23,
      "uuid": 5797204
    },
    {
      "user": "nturaga",
      "count": 10,
      "uuid": 2746443
    },
    {
      "user": "felixernst",
      "count": 2,
      "uuid": 17824332
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "kant",
      "count": 1,
      "uuid": 32717
    },
    {
      "user": "kayla-morrell",
      "count": 1,
      "uuid": 32339524
    },
    {
      "user": "mikemc",
      "count": 1,
      "uuid": 5105005
    },
    {
      "user": "tuomasborman",
      "count": 1,
      "uuid": 60338854
    },
    {
      "user": "dave1618",
      "count": 1,
      "uuid": 13027579
    },
    {
      "user": "nbokulich",
      "count": 1,
      "uuid": 1907564
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2666,
    "source": "https://www.bioconductor.org/packages/stats/bioc/decontam"
  },
  "_mentions": 76,
  "_devurl": "https://github.com/benjjneb/decontam",
  "_searchresults": 740,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/decontam.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/benjjneb/decontam",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "isContaminant",
    "isNotContaminant",
    "plot_condition",
    "plot_frequency"
  ],
  "_help": [
    {
      "page": "isContaminant",
      "title": "Identify contaminant sequences.",
      "topics": [
        "isContaminant",
        "isContaminant,ANY-method"
      ]
    },
    {
      "page": "isNotContaminant",
      "title": "Identify non-contaminant sequences.",
      "topics": [
        "isNotContaminant",
        "isNotContaminant,ANY-method"
      ]
    },
    {
      "page": "plot_condition",
      "title": "Plot DNA concentrations as a function of experimental conditions.",
      "topics": [
        "plot_condition"
      ]
    },
    {
      "page": "plot_frequency",
      "title": "Plot frequencies as a function of input DNA concentration",
      "topics": [
        "plot_frequency"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "magrittr",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "decontam_intro.Rmd",
      "filename": "decontam_intro.html",
      "title": "Introduction to decontam",
      "author": "Benjamin Callahan, Nicole Davis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Identifying contaminants in marker-gene and metagenomics data",
        "Introduction",
        "Necessary Ingredients",
        "Setting up",
        "Inspect Library Sizes",
        "Identify Contaminants - Frequency",
        "Identify Contaminants - Prevalence",
        "Putting It All Together",
        "Conclusion"
      ],
      "created": "2017-07-28 17:27:10",
      "modified": "2020-07-06 16:38:34",
      "commits": 10
    }
  ],
  "_score": 11.214724244463264,
  "_indexed": false,
  "_nocasepkg": "decontam",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/decontam",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.32.0",
      "date": "2026-06-08T07:14:33.000Z",
      "distro": "noble",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "835033ae1c75c89ec630e6dd2f7ed7a577db1241e5f0de1ab9e793893f467850",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.32.0",
      "date": "2026-06-08T07:14:37.000Z",
      "distro": "noble",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "5e26df0d2f418e1a7a1e0a36198efdb919c9b2186c4096264d522ba53705916a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.32.0",
      "date": "2026-06-08T07:13:49.000Z",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "a413b9f3d680cf8a425738c1f1fdb322dd96799259aa9cea3a870bca10e25458",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.32.0",
      "date": "2026-06-08T07:13:34.000Z",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "e7f1b9712decb8b407a640b111365d560e10bc8cbf89bfa8a152f7075e63abed",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.32.0",
      "date": "2026-06-08T07:13:37.000Z",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "1643bf87e10fff69781ca13509274efe196f93a1296f0d20822f61f6436c6cfa",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-06-08T07:12:53.000Z",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "c96dcec6e475d963a194b1c4d99ff3d8b093642075547bff34a5f09e8ae76b90",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-06-08T07:12:48.000Z",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "18d6e8b293f68f6374d01e5027e6c39f7868968d332a3a044c29cbc95d593442",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.32.0",
      "date": "2026-06-08T07:12:55.000Z",
      "commit": "783a69b26ad74d418fa79b5cf597a68df39f7119",
      "fileid": "da8702f7c321adcf75849d8cf84818e6eaaf6f056e0498be0633e91f48b9b133",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121560946"
    }
  ]
}