{
  "_id": "6ae767891e2c7b3a4f5303b8",
  "Package": "MassArray",
  "Type": "Package",
  "Title": "Analytical Tools for MassArray Data",
  "Version": "1.65.0",
  "Date": "2019-03-18",
  "Author": "Reid F. Thompson <reid.thompson@gmail.com>, John M. Greally\n<john.greally@einstein.yu.edu>",
  "Maintainer": "Reid F. Thompson <reid.thompson@gmail.com>",
  "Description": "This package is designed for the import, quality control,\nanalysis, and visualization of methylation data generated using\nSequenom's MassArray platform.  The tools herein contain a\nhighly detailed amplicon prediction for optimal assay design.\nAlso included are quality control measures of data, such as\nprimer dimer and bisulfite conversion efficiency estimation.\nMethylation data are calculated using the same algorithms\ncontained in the EpiTyper software package.  Additionally,\nautomatic SNP-detection can be used to flag potentially\nconfounded data from specific CG sites.  Visualization includes\nbarplots of methylation data as well as UCSC Genome\nBrowser-compatible BED tracks.  Multiple assays can be\npositionally combined for integrated analysis.",
  "License": "GPL (>=2)",
  "biocViews": "ImmunoOncology, DNAMethylation, SNP, MassSpectrometry,\nGenetics, DataImport, Visualization",
  "LazyData": "yes",
  "LazyLoad": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:27 UTC",
  "RemoteUrl": "https://github.com/bioc/MassArray",
  "RemoteRef": "HEAD",
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    "User": "root"
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  "_type": "src",
  "_file": "MassArray_1.65.0.tar.gz",
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  "_expires": "2027-02-09T16:23:35.000Z",
  "_created": "2026-11-01T13:54:15.000Z",
  "_published": "2026-11-01T16:23:37.563Z",
  "_upstream": "https://github.com/bioc/MassArray",
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  "_maintainer": {
    "name": "Reid F. Thompson",
    "email": "reid.thompson@gmail.com",
    "login": "reidt03",
    "description": "",
    "uuid": 21960505
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    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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      "role": "Depends"
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    {
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    {
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    },
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  "_selfowned": true,
  "_usedby": 0,
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      "n": 2
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  "_tags": [],
  "_bioc": [
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    },
    {
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      "bioc": "3.23",
      "repository": "bioc"
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  ],
  "_topics": [
    "immunooncology",
    "dnamethylation",
    "snp",
    "massspectrometry",
    "genetics",
    "dataimport",
    "visualization"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_downloads": {
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    "source": "https://www.bioconductor.org/packages/stats/bioc/MassArray"
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  "_mentions": 84,
  "_searchresults": 6,
  "_abi": {
    "exports": [
      {
        "key": "MassArray::MassArrayData",
        "hash": "9e32fb2c01326592"
      },
      {
        "key": "MassArray::MassArrayFragment",
        "hash": "4abb6da382d4f4fd"
      },
      {
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        "hash": "e625cab0e8753668"
      },
      {
        "key": "MassArray::MassArraySpectrum",
        "hash": "280a57c9d583eb75"
      },
      {
        "key": "MassArray::generic:combine",
        "hash": "ee9c69fbcf551ee0"
      },
      {
        "key": "MassArray::generic:position",
        "hash": "1450b6f1e1fd9b2e"
      },
      {
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        "hash": "aac7fe2e7f958c5a"
      },
      {
        "key": "MassArray::generic:revComplement",
        "hash": "0ee23c4856a4a368"
      },
      {
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        "hash": "d02de789d4ab0ffa"
      },
      {
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        "hash": "34bd5bd576b2a0d2"
      }
    ],
    "imports": []
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/MassArray.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "ampliconPrediction",
    "analyzeCpGs",
    "bisConvert",
    "calcMeth",
    "calcMW",
    "calcPercentAdduct",
    "calcPercentConversion",
    "combine",
    "convControl",
    "countCGs",
    "createWiggle",
    "estimatePrimerDimer",
    "evaluateSNPs",
    "expandSequence",
    "findCollisions",
    "findFragments",
    "findPeaks",
    "identifySNPs",
    "importEpiTyperData",
    "importEpiTyperData.new",
    "inSilicoFragmentation",
    "isAssayable",
    "numCollisions",
    "plot.MassArrayData",
    "position",
    "position<-",
    "revComplement",
    "rnaDigest",
    "samples",
    "samples<-",
    "sum.MassArraySpectrum"
  ],
  "_datasets": [
    {
      "name": "MassArray.example.data",
      "title": "MassArray Data object",
      "object": "MassArray.example.data",
      "class": [
        "MassArrayData"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ampliconPrediction",
      "title": "Amplicon prediction",
      "topics": [
        "ampliconPrediction"
      ]
    },
    {
      "page": "analyzeCpGs",
      "title": "Analyze CG methylation",
      "topics": [
        "analyzeCpGs"
      ]
    },
    {
      "page": "bisConvert",
      "title": "Bisulphite conversion",
      "topics": [
        "bisConvert"
      ]
    },
    {
      "page": "calcMeth",
      "title": "Calculate percent methylation",
      "topics": [
        "calcMeth"
      ]
    },
    {
      "page": "calcMW",
      "title": "Calculate molecular weight",
      "topics": [
        "calcMW"
      ]
    },
    {
      "page": "calcPercentAdduct",
      "title": "Calculate percent salt adducts",
      "topics": [
        "calcPercentAdduct"
      ]
    },
    {
      "page": "calcPercentConversion",
      "title": "Calculate percent conversion",
      "topics": [
        "calcPercentConversion"
      ]
    },
    {
      "page": "combine",
      "title": "Combine MassArrayData objects",
      "topics": [
        "combine"
      ]
    },
    {
      "page": "combine-methods",
      "title": "Combine MassArrayData objects (methods)",
      "topics": [
        "combine,MassArrayData,MassArrayData-method",
        "combine,MassArrayData,missing-method",
        "combine-methods"
      ]
    },
    {
      "page": "convControl",
      "title": "Conversion control",
      "topics": [
        "convControl"
      ]
    },
    {
      "page": "countCGs",
      "title": "Count number of CGs",
      "topics": [
        "countCGs"
      ]
    },
    {
      "page": "createWiggle",
      "title": "Create wiggle track",
      "topics": [
        "createWiggle"
      ]
    },
    {
      "page": "estimatePrimerDimer",
      "title": "Estimate Primer Dimers",
      "topics": [
        "estimatePrimerDimer"
      ]
    },
    {
      "page": "evaluateSNPs",
      "title": "Evaluate SNPs",
      "topics": [
        "evaluateSNPs"
      ]
    },
    {
      "page": "expandSequence",
      "title": "Expand nucleotide sequence",
      "topics": [
        "expandSequence"
      ]
    },
    {
      "page": "findCollisions",
      "title": "Find peak collisions",
      "topics": [
        "findCollisions"
      ]
    },
    {
      "page": "findFragments",
      "title": "Find fragments",
      "topics": [
        "findFragments"
      ]
    },
    {
      "page": "findPeaks",
      "title": "Find peaks",
      "topics": [
        "findPeaks"
      ]
    },
    {
      "page": "identifySNPs",
      "title": "Identify SNPs",
      "topics": [
        "identifySNPs"
      ]
    },
    {
      "page": "importEpiTyperData",
      "title": "Import EpiTyper data (v.1.0)",
      "topics": [
        "importEpiTyperData"
      ]
    },
    {
      "page": "importEpiTyperData.new",
      "title": "Import EpiTyper data (v.1.0.5)",
      "topics": [
        "importEpiTyperData.new"
      ]
    },
    {
      "page": "inSilicoFragmentation",
      "title": "In silico fragmentation",
      "topics": [
        "inSilicoFragmentation"
      ]
    },
    {
      "page": "isAssayable",
      "title": "Is assayable?",
      "topics": [
        "isAssayable"
      ]
    },
    {
      "page": "MassArray.example.data",
      "title": "MassArray Data object",
      "topics": [
        "MassArray.example.data"
      ]
    },
    {
      "page": "MassArrayData-class",
      "title": "Class \"MassArrayData\"",
      "topics": [
        "$,MassArrayData-method",
        "$<-,MassArrayData-method",
        "initialize,MassArrayData-method",
        "MassArrayData-class",
        "[,MassArrayData-method"
      ]
    },
    {
      "page": "MassArrayFragment-class",
      "title": "Class \"MassArrayFragment\"",
      "topics": [
        "$,MassArrayFragment-method",
        "$<-,MassArrayFragment-method",
        "initialize,MassArrayFragment-method",
        "MassArrayFragment-class"
      ]
    },
    {
      "page": "MassArrayPeak-class",
      "title": "Class \"MassArrayPeak\"",
      "topics": [
        "$,MassArrayPeak-method",
        "$<-,MassArrayPeak-method",
        "initialize,MassArrayPeak-method",
        "MassArrayPeak-class"
      ]
    },
    {
      "page": "MassArraySpectrum-class",
      "title": "Class \"MassArraySpectrum\"",
      "topics": [
        "$,MassArraySpectrum-method",
        "$<-,MassArraySpectrum-method",
        "initialize,MassArraySpectrum-method",
        "MassArraySpectrum-class"
      ]
    },
    {
      "page": "numCollisions",
      "title": "Count peak collisions",
      "topics": [
        "numCollisions"
      ]
    },
    {
      "page": "plot.MassArrayData",
      "title": "Plot MassArrayData",
      "topics": [
        "plot.MassArrayData"
      ]
    },
    {
      "page": "position",
      "title": "Operate on positional information",
      "topics": [
        "position",
        "position<-"
      ]
    },
    {
      "page": "position-methods",
      "title": "Operate on positional information (methods)",
      "topics": [
        "position,MassArrayData-method",
        "position-methods",
        "position<-,MassArrayData,character-method",
        "position<-,MassArrayData,missing-method"
      ]
    },
    {
      "page": "revComplement",
      "title": "Reverse complement",
      "topics": [
        "revComplement"
      ]
    },
    {
      "page": "revComplement-methods",
      "title": "Reverse complement (methods)",
      "topics": [
        "revComplement,character-method",
        "revComplement,MassArrayData-method",
        "revComplement-methods"
      ]
    },
    {
      "page": "rnaDigest",
      "title": "RNA digest",
      "topics": [
        "rnaDigest"
      ]
    },
    {
      "page": "samples",
      "title": "Operate on sample name(s)",
      "topics": [
        "samples",
        "samples<-"
      ]
    },
    {
      "page": "samples-methods",
      "title": "Operate on sample name(s) (methods)",
      "topics": [
        "samples,MassArrayData-method",
        "samples-methods",
        "samples<-,MassArrayData,character-method",
        "samples<-,MassArrayData,missing-method"
      ]
    },
    {
      "page": "sum.MassArraySpectrum",
      "title": "Sum MassArraySpectrum objects",
      "topics": [
        "sum.MassArraySpectrum"
      ]
    }
  ],
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      "source": "MassArray.Rnw",
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        "Changes for MassArray in current BioC release",
        "Optimal Amplicon Design",
        "Conversion Controls",
        "Data Import",
        "Data Visualization",
        "Single Nucleotide Polymorphism Detection",
        "Previous Release Notes"
      ],
      "created": "2013-11-01 20:12:13",
      "modified": "2019-12-23 23:23:51",
      "commits": 2
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