{
  "_id": "6ac0c3ee91601a2ad2998934",
  "Package": "PlasmaMutationDetector",
  "Type": "Package",
  "Title": "Tumor Mutation Detection in Plasma",
  "Version": "1.7.2",
  "Date": "2018-05-16",
  "Author": "Yves Rozenholc, Nicolas Pécuchet, Pierre Laurent-Puig",
  "Maintainer": "Yves Rozenholc <yves.rozenholc@parisdescartes.fr>",
  "Description": "Aims at detecting single nucleotide variation (SNV) and\ninsertion/deletion (INDEL) in circulating tumor DNA (ctDNA),\nused as a surrogate marker for tumor, at each base position of\nan Next Generation Sequencing (NGS) analysis. Mutations are\nassessed by comparing the minor-allele frequency at each\nposition to the measured PER in control samples.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "6.0.1",
  "LazyData": "true",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-03 08:52:36 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libbz2-dev liblzma-dev libssl-dev xz-utils\nzlib1g-dev",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2018-06-11 06:43:09 UTC",
  "RemoteUrl": "https://github.com/cran/PlasmaMutationDetector",
  "RemoteRef": "HEAD",
  "RemoteSha": "9a5b641f806d9f6b66411a71205ebd1d83f4ee75",
  "_user": "cran",
  "_type": "src",
  "_file": "PlasmaMutationDetector_1.7.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/f0721de30aa924e69473ae6efa44b4c34fe3833b2b5d98ba462193b3d5bb7739",
  "_filesize": 4030297,
  "_sha256": "f0721de30aa924e69473ae6efa44b4c34fe3833b2b5d98ba462193b3d5bb7739",
  "_expires": "2027-01-11T08:59:24.000Z",
  "_created": "2026-10-03T08:52:36.000Z",
  "_published": "2026-10-03T08:59:25.974Z",
  "_jobs": [
    {
      "job": 111169316974,
      "time": 326,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11269049326"
    },
    {
      "job": 111169316980,
      "time": 271,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11269468780"
    },
    {
      "job": 111168602590,
      "time": 272,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11269123879"
    },
    {
      "job": 111169317035,
      "time": 136,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11269882792"
    },
    {
      "job": 111169316997,
      "time": 282,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11269583378"
    },
    {
      "job": 111169316992,
      "time": 285,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11269803034"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/37110932611",
  "_status": "success",
  "_upstream": "https://github.com/cran/PlasmaMutationDetector",
  "_commit": {
    "id": "9a5b641f806d9f6b66411a71205ebd1d83f4ee75",
    "author": "Yves Rozenholc <yves.rozenholc@parisdescartes.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.7.2\n",
    "time": 1528699389
  },
  "_maintainer": {
    "name": "Yves Rozenholc",
    "email": "yves.rozenholc@parisdescartes.fr"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.2.0",
      "role": "Depends"
    },
    {
      "package": "grid",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.30.0",
      "role": "Depends"
    },
    {
      "package": "VariantAnnotation",
      "version": ">= 1.24.0",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.16.0",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "version": ">= 1.30.0",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "version": ">= 1.38.0",
      "role": "Imports"
    },
    {
      "package": "robustbase",
      "version": ">= 0.92-8",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "version": ">= 1.8.0",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 630,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 332,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PlasmaMutationDetector"
  },
  "_mentions": 2,
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/PlasmaMutationDetector.html",
    "LICENSE"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.5.2",
      "date": "2016-09-09"
    },
    {
      "version": "1.6.2",
      "date": "2017-11-15"
    },
    {
      "version": "1.6.10",
      "date": "2018-01-26"
    },
    {
      "version": "1.7.0",
      "date": "2018-04-26"
    },
    {
      "version": "1.7.1",
      "date": "2018-05-16"
    },
    {
      "version": "1.7.2",
      "date": "2018-06-11"
    }
  ],
  "_exports": [
    "BuildCtrlErrorRate",
    "DetectPlasmaMutation",
    "MAF_from_BAM",
    "PrepareLibrary"
  ],
  "_datasets": [
    {
      "name": "background_error_rate",
      "title": "The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file 'background_error_rate.txt'.",
      "object": "background_error_rate",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrpos",
        "N0",
        "E0",
        "p.sain",
        "up.sain",
        "E0indel",
        "indel.p.sain",
        "indel.up.sain",
        "REF",
        "hotspot"
      ],
      "rows": 10199,
      "table": true,
      "tojson": true
    },
    {
      "name": "hotspot",
      "title": "The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a txt file 'hotspot.txt' which contains a vector/variable -named chrpos (first row)- of chars, of the form chrN:XXXXXXXXX defining genomic positions.",
      "object": "hotspot",
      "class": [
        "data.frame"
      ],
      "fields": [
        "chrpos"
      ],
      "rows": 44,
      "table": true,
      "tojson": true
    },
    {
      "name": "pos_ind",
      "title": "The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.",
      "object": "positions_ranges",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "pos_ranges",
      "title": "The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.",
      "object": "positions_ranges",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pos_snp",
      "title": "The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.",
      "object": "positions_ranges",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "background_error_rate",
      "title": "The package provide the SNV and INDEL PERs computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 from 29 controls in a table available in the data file 'background_error_rate.txt'.",
      "topics": [
        "background_error_rate",
        "background_error_rate.txt"
      ]
    },
    {
      "page": "BuildCtrlErrorRate",
      "title": "function BuildCtrlErrorRate",
      "topics": [
        "BuildCtrlErrorRate"
      ]
    },
    {
      "page": "DetectPlasmaMutation",
      "title": "function DetectPlasmaMutation",
      "topics": [
        "DetectPlasmaMutation"
      ]
    },
    {
      "page": "hotspot",
      "title": "The package provide a list of known hotspot positions located on the amplicons of the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a txt file 'hotspot.txt' which contains a vector/variable -named chrpos (first row)- of chars, of the form chrN:XXXXXXXXX defining genomic positions.",
      "topics": [
        "hotspot",
        "hotspot.txt"
      ]
    },
    {
      "page": "LoadBackgroundErrorRate",
      "title": "function LoadBackgroundErrorRate",
      "topics": [
        "LoadBackgroundErrorRate"
      ]
    },
    {
      "page": "MAF_from_BAM",
      "title": "function MAF_from_BAM",
      "topics": [
        "MAF_from_BAM"
      ]
    },
    {
      "page": "positions_ranges",
      "title": "The package provide the positions and ranges computed for the Ion AmpliSeq™ Colon and Lung Cancer Panel v2 as a Rdata file 'positions_ranges.rda'.",
      "topics": [
        "positions_ranges",
        "positions_ranges.rda",
        "pos_ind",
        "pos_ranges",
        "pos_snp"
      ]
    },
    {
      "page": "PrepareLibrary",
      "title": "function PrepareLibrary",
      "topics": [
        "PrepareLibrary"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "DEoptimR",
    "farver",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "RColorBrewer",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "robustbase",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_score": 1.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "plasmamutationdetector",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.2",
      "date": "2026-10-03T08:55:31.000Z",
      "distro": "resolute",
      "commit": "9a5b641f806d9f6b66411a71205ebd1d83f4ee75",
      "fileid": "https://r2.ropensci.org/381d59dca29c68ecc1bff35cdc42a331f0988ae9873dcd367ce283e40f796739",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37110932611"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.7.2",
      "date": "2026-10-03T08:55:26.000Z",
      "distro": "resolute",
      "commit": "9a5b641f806d9f6b66411a71205ebd1d83f4ee75",
      "fileid": "https://r2.ropensci.org/910b88f25aa2c71d21a0f08e61ec46a6bc97f35b92ad056eec9d32bf213361ed",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37110932611"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7.2",
      "date": "2026-10-03T08:55:37.000Z",
      "commit": "9a5b641f806d9f6b66411a71205ebd1d83f4ee75",
      "fileid": "https://r2.ropensci.org/a586d34270ed87c9e8fd423bb9d87900783227e3f29024b2288041177d84a39b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37110932611"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.2",
      "date": "2026-10-03T08:54:58.000Z",
      "commit": "9a5b641f806d9f6b66411a71205ebd1d83f4ee75",
      "fileid": "https://r2.ropensci.org/f3e44860ffb2797e899775cb7a7ab52626afab2acb51cc34c8f290d6addae907",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37110932611"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.7.2",
      "date": "2026-10-03T08:54:37.000Z",
      "commit": "9a5b641f806d9f6b66411a71205ebd1d83f4ee75",
      "fileid": "https://r2.ropensci.org/b774bb49cc11cee46eedf172d80c27bd798dfcb50adf5ae2f8134029acaa4a29",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/37110932611"
    }
  ]
}