{
  "_id": "6a106c3bacfb0bcc41caa7dd",
  "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": "2026-05-07 08:56:32 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",
  "MD5sum": "209e39eea396e74bb56a68cc10180197",
  "_user": "cran",
  "_type": "src",
  "_file": "PlasmaMutationDetector_1.7.2.tar.gz",
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  "_created": "2026-05-07T08:56:32.000Z",
  "_published": "2026-05-22T14:46:19.957Z",
  "_distro": "noble",
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  "_status": "success",
  "_host": "GitHub-Actions",
  "_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
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  "_maintainer": {
    "name": "Yves Rozenholc",
    "email": "yves.rozenholc@parisdescartes.fr"
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  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
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    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PlasmaMutationDetector"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
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    "manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
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      "date": "2016-09-09"
    },
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      "date": "2017-11-15"
    },
    {
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      "date": "2018-01-26"
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      "date": "2018-04-26"
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      "date": "2018-05-16"
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      "date": "2018-06-11"
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  "_exports": [
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    "DetectPlasmaMutation",
    "MAF_from_BAM",
    "PrepareLibrary"
  ],
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      "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",
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        "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",
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      ],
      "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"
      ]
    },
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      "page": "MAF_from_BAM",
      "title": "function MAF_from_BAM",
      "topics": [
        "MAF_from_BAM"
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    },
    {
      "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"
      ]
    }
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    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
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    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
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    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
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    "S7",
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    "SummarizedExperiment",
    "sys",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
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  "_indexed": true,
  "_nocasepkg": "plasmamutationdetector",
  "_universes": [
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