{
  "_id": "6a1ad4471d7bb097a09e405f",
  "Package": "DNABarcodeCompatibility",
  "Type": "Package",
  "Title": "A Tool for Optimizing Combinations of DNA Barcodes Used in\nMultiplexed Experiments on Next Generation Sequencing Platforms",
  "Version": "1.29.0",
  "Maintainer": "Céline Trébeau <ctrebeau@pasteur.fr>",
  "Authors@R": "c(\nperson(\"Céline\", \"Trébeau\", email = \"ctrebeau@pasteur.fr\", role = \"cre\", comment = c(ORCID = \"0000-0001-6795-5379\")),\nperson(\"Jacques\", \"Boutet de Monvel\", email = \"jacques.boutet-de-monvel@pasteur.fr\", role = \"aut\", comment = c(ORCID = \"0000-0001-6182-3527\")),\nperson(\"Fabienne\", \"Wong Jun Tai\", email = \"virginie.wong-jun-tai@pasteur.fr\", role = \"ctb\"),\nperson(\"Raphaël\", \"Etournay\", email = \"raphael.etournay@pasteur.fr\", role = \"aut\", comment = c(ORCID = \"0000-0002-2441-9274\")))",
  "Description": "The package allows one to obtain optimised combinations of\nDNA barcodes to be used for multiplex sequencing. In each\nbarcode combination, barcodes are pooled with respect to\nIllumina chemistry constraints. Combinations can be filtered to\nkeep those that are robust against substitution and\ninsertion/deletion errors thereby facilitating the\ndemultiplexing step. In addition, the package provides an\noptimiser function to further favor the selection of barcode\ncombinations with least heterogeneity in barcode usage.",
  "License": "file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "6.1.1",
  "VignetteBuilder": "knitr",
  "biocViews": "Preprocessing, Sequencing",
  "URL": "https://dnabarcodecompatibility.pasteur.fr/",
  "BugReports": "https://gitlab.pasteur.fr/ida-public/dnabarcodecompatibility/-/issues",
  "NeedsCompilation": "yes",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:15 UTC",
  "RemoteUrl": "https://github.com/bioc/DNABarcodeCompatibility",
  "RemoteRef": "HEAD",
  "RemoteSha": "14bac8025e765e567584333226b9d614382be39d",
  "Packaged": {
    "Date": "2026-05-30 08:41:10 UTC",
    "User": "root"
  },
  "Author": "Céline Trébeau [cre] (ORCID: <https://orcid.org/0000-0001-6795-5379>),\nJacques Boutet de Monvel [aut] (ORCID:\n<https://orcid.org/0000-0001-6182-3527>),\nFabienne Wong Jun Tai [ctb],\nRaphaël Etournay [aut] (ORCID: <https://orcid.org/0000-0002-2441-9274>)",
  "MD5sum": "3f72b285667924a2d8ef9f81523735b5",
  "_user": "bioc",
  "_type": "src",
  "_file": "DNABarcodeCompatibility_1.29.0.tar.gz",
  "_fileid": "73b01b0fb43d7d21e1b32f855c47bae175d050ee88f3b6401b75aa9ab06e8fe3",
  "_filesize": 211386,
  "_sha256": "73b01b0fb43d7d21e1b32f855c47bae175d050ee88f3b6401b75aa9ab06e8fe3",
  "_created": "2026-05-30T08:41:10.000Z",
  "_published": "2026-05-30T12:12:54.998Z",
  "_jobs": [
    {
      "job": 78637239152,
      "time": 161,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306919702"
    },
    {
      "job": 78637239123,
      "time": 203,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306923656"
    },
    {
      "job": 78637239111,
      "time": 210,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306924157"
    },
    {
      "job": 78637239137,
      "time": 177,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306921153"
    },
    {
      "job": 78637239134,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306921681"
    },
    {
      "job": 78637239127,
      "time": 110,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308076891"
    },
    {
      "job": 78637239117,
      "time": 347,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306938126"
    },
    {
      "job": 78637239116,
      "time": 151,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308079556"
    },
    {
      "job": 78637239118,
      "time": 229,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306928054"
    },
    {
      "job": 78637001416,
      "time": 294,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306903884"
    },
    {
      "job": 78637239100,
      "time": 123,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306916214"
    },
    {
      "job": 78637239139,
      "time": 171,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306920872"
    },
    {
      "job": 78637239128,
      "time": 141,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306917997"
    },
    {
      "job": 78637239110,
      "time": 172,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306920670"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/DNABarcodeCompatibility",
  "_commit": {
    "id": "14bac8025e765e567584333226b9d614382be39d",
    "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": 1777380555
  },
  "_maintainer": {
    "name": "Céline Trébeau",
    "email": "ctrebeau@pasteur.fr",
    "login": "celinetrebeau",
    "description": "",
    "uuid": 37372810,
    "orcid": "0000-0001-6795-5379"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "numbers",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.11.2",
      "role": "Imports"
    },
    {
      "package": "BH",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "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": [
    "preprocessing",
    "sequencing",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 312,
    "source": "https://www.bioconductor.org/packages/stats/bioc/DNABarcodeCompatibility"
  },
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DNABarcodeCompatibility.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/comoto-pasteur-fr/dnabarcodecompatibility",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "distance",
    "distance_filter",
    "experiment_design",
    "file_loading_and_checking",
    "get_all_combinations",
    "get_random_combinations",
    "optimize_combinations"
  ],
  "_datasets": [
    {
      "name": "IlluminaIndexes",
      "title": "Barcode dataset from Illumina with features.",
      "object": "IlluminaIndexes",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Id",
        "sequence",
        "GC_content",
        "homopolymer"
      ],
      "rows": 48,
      "table": true,
      "tojson": true
    },
    {
      "name": "IlluminaIndexesRaw",
      "title": "Barcode dataset from Illumina.",
      "object": "IlluminaIndexesRaw",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2"
      ],
      "rows": 48,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "DNABarcodeCompatibility-package",
      "title": "DNABarcodeCompatibility: to find optimised sets of compatible barcodes with least heterogeneity in barcode usage for multiplex experiments performed on next generation sequencing platforms.",
      "topics": [
        "DNABarcodeCompatibility-package"
      ]
    },
    {
      "page": "distance",
      "title": "Calculate distance between two barcodes.",
      "topics": [
        "distance"
      ]
    },
    {
      "page": "distance_filter",
      "title": "Select barcode combinations with error correction properties",
      "topics": [
        "distance_filter"
      ]
    },
    {
      "page": "experiment_design",
      "title": "Find a set of barcode combinations with least heterogeneity in barcode usage for single and dual indexing",
      "topics": [
        "experiment_design"
      ]
    },
    {
      "page": "file_loading_and_checking",
      "title": "Loading and checking DNA barcodes.",
      "topics": [
        "file_loading_and_checking"
      ]
    },
    {
      "page": "get_all_combinations",
      "title": "Get all compatible combinations.",
      "topics": [
        "get_all_combinations"
      ]
    },
    {
      "page": "get_random_combinations",
      "title": "Get a large set of compatible combinations.",
      "topics": [
        "get_random_combinations"
      ]
    },
    {
      "page": "IlluminaIndexes",
      "title": "Barcode dataset from Illumina with features.",
      "topics": [
        "IlluminaIndexes"
      ]
    },
    {
      "page": "IlluminaIndexesRaw",
      "title": "Barcode dataset from Illumina.",
      "topics": [
        "IlluminaIndexesRaw"
      ]
    },
    {
      "page": "optimize_combinations",
      "title": "Find a set of barcode combinations with least heterogeneity in barcode usage",
      "topics": [
        "optimize_combinations"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/DNABarcodeCompatibility/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "cli",
    "cpp11",
    "dplyr",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "numbers",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "Rcpp",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Introduction to DNABarcodeCompatibility",
      "author": "Céline Trébeau, Jacques Boutet de Monvel, Fabienne Wong Jun Tai, Raphaël Etournay",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load the package",
        "Define a helper function to save the raw dataset as a temporary text file",
        "Design an experiment",
        "Examples for single indexing",
        "Examples for dual indexing",
        "Build your own workflow",
        "Load and check a dataset of barcodes",
        "Examples of an exhaustive search of compatible barcode combinations",
        "Examples of a random search of compatible barcode combinations",
        "Constrain barcodes to be robust against one substitution error",
        "Optimize the set of compatible combinations to reduce barcode redundancy",
        "The optimized result isn't an optimum when filtering out too many barcodes"
      ],
      "created": "2024-09-11 10:21:07",
      "modified": "2024-09-11 10:21:07",
      "commits": 1
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "dnabarcodecompatibility",
  "_universes": [
    "bioc",
    "celinetrebeau"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:44:28.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "0f5690fbe027248a63ee3a23ce3b409902a32139fe7934b050b0a8d5fa8d5dee",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:44:40.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "d2dc588012213360e331c60ed57f864dc49aa9beecc13c31b96cb674c193d2e7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:44:03.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "64e3c33884033a377ffae958a1ad80a27a4465328053c2f9e3fdade822c7d38a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-05-30T08:44:09.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "bbb404e87120eb6e484837dd3846cf7b00f0636f1b040080189ae02484371179",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T12:11:36.000Z",
      "arch": "aarch64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "e563c670e19945aa89f3ade8a3db9430516d43b5e6d69d7890390b0b47bd6293",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T08:46:10.000Z",
      "arch": "x86_64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "304390fb6b298632e333e6aab98b99ede9715f1e2bb5e12550e1ba9ba4a8b024",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T12:11:47.000Z",
      "arch": "aarch64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "fb87e62cfa66311147497796901199c98b60494c4c5d056ff1be2bfd76942942",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-05-30T08:44:51.000Z",
      "arch": "x86_64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "973781ecde66aff8e57579cfc0bee24a261677542d049cd51d8e3c0bb32d401c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.29.0",
      "date": "2026-05-30T08:43:35.000Z",
      "arch": "emscripten",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "32acc13c8eb5daee295e53216ba50879bd2f074e746c61c567723218a2993f44",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-30T08:43:19.000Z",
      "arch": "x86_64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "a22a3bce5a2aec529e5a671e0bc38cdc3137ceabe574338829ad680e0cbf8bc5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-30T08:42:58.000Z",
      "arch": "x86_64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "405aeff7a8d07b7be683ecc8168a86e2aa628f9093972c182ab818a28a01bd37",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-05-30T08:43:18.000Z",
      "arch": "x86_64",
      "commit": "14bac8025e765e567584333226b9d614382be39d",
      "fileid": "c99129807e716558f6be2fe0f66f1bd45d0001ecc5f5a3c11961e0892fb25169",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679397807"
    }
  ]
}