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  "Package": "DEploid",
  "Type": "Package",
  "Title": "Deconvolute Mixed Genomes with Unknown Proportions",
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  "Authors@R": "c(\nperson(\"Joe\", \"Zhu\", , \"sha.joe.zhu@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7566-2787\")),\nperson('Jacob', 'Almagro-Garcia', role=c('aut')),\nperson('Gil', 'McVean', role=c('aut')),\nperson('University of Oxford', '', role=c('cph')),\nperson('Yinghan', 'Liu', role=c('ctb')),\nperson('CodeCogs', 'Zyba Ltd', role=c('com', \"cph\")),\nperson('Deepak', 'Bandyopadhyay', role=c('com', \"cph\")),\nperson('Lutz', 'Kettner', role=c('com', \"cph\"))\n)",
  "Description": "Traditional phasing programs are limited to diploid\norganisms. Our method modifies Li and Stephens algorithm with\nMarkov chain Monte Carlo (MCMC) approaches, and builds a\ngeneric framework that allows haplotype searches in a multiple\ninfection setting. This package is primarily developed as part\nof the Pf3k project, which is a global collaboration using the\nlatest sequencing technologies to provide a high-resolution\nview of natural variation in the malaria parasite Plasmodium\nfalciparum. Parasite DNA are extracted from patient blood\nsample, which often contains more than one parasite strain,\nwith unknown proportions. This package is used for\ndeconvoluting mixed haplotypes, and reporting the mixture\nproportions from each sample.",
  "URL": "https://github.com/DEploid-dev/DEploid-r",
  "BugReports": "https://github.com/DEploid-dev/DEploid-r/issues",
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  "Date": "2024-12-22",
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  "Author": "Joe Zhu [aut, cre] (<https://orcid.org/0000-0001-7566-2787>),\nJacob Almagro-Garcia [aut], Gil McVean [aut], University of\nOxford [cph], Yinghan Liu [ctb], CodeCogs Zyba Ltd [com, cph],\nDeepak Bandyopadhyay [com, cph], Lutz Kettner [com, cph]",
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    "description": "Programmer, data scientist, statistician. Made in China, built in NZ, upgraded in Oxford",
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  "_devurl": "https://github.com/deploid-dev/deploid-r",
  "_searchresults": 42,
  "_topics": [
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    "cpp"
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/contents.json",
    "extra/DEploid.html",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
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  "_realowner": "deploid-dev",
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      "date": "2016-11-25"
    },
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    },
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      "date": "2017-08-09"
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      "date": "2017-08-09"
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      "version": "0.4.4",
      "date": "2017-09-01"
    },
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      "date": "2018-05-18"
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      "date": "2018-10-21"
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      "date": "2018-10-23"
    },
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      "date": "2020-04-21"
    },
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    "computeObsWSAF",
    "dEploid",
    "extractCoverageFromTxt",
    "extractCoverageFromVcf",
    "extractPLAF",
    "haplotypePainter",
    "histWSAF",
    "plotAltVsRef",
    "plotAltVsRefPlotly",
    "plotHistWSAFPlotly",
    "plotObsExpWSAF",
    "plotObsExpWSAFPlotly",
    "plotProportions",
    "plotWSAFvsPLAF",
    "plotWSAFVsPLAFPlotly"
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    {
      "page": "dEploid",
      "title": "Deconvolute mixed haplotypes",
      "topics": [
        "dEploid"
      ]
    },
    {
      "page": "plotAltVsRefPlotly",
      "title": "Plot coverage",
      "topics": [
        "plotAltVsRefPlotly"
      ]
    },
    {
      "page": "plotHistWSAFPlotly",
      "title": "WSAF histogram",
      "topics": [
        "plotHistWSAFPlotly"
      ]
    },
    {
      "page": "plotObsExpWSAFPlotly",
      "title": "Plot WSAF",
      "topics": [
        "plotObsExpWSAFPlotly"
      ]
    },
    {
      "page": "plotWSAFVsPLAFPlotly",
      "title": "Plot WSAF vs PLAF",
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      ]
    }
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      "description": "compression library - runtime"
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      "shlib": "libstdc++",
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      "filename": "dEploid-Arguments.html",
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      "author": "Sha Zhu",
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        "You may also try",
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        "Reporting Bugs",
        "Citing DEploid"
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      "modified": "2024-12-23 15:30:15",
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