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  "Type": "Package",
  "Title": "Deconvolute Mixed Genomes with Unknown Proportions",
  "Version": "0.5.7",
  "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",
  "License": "GPL (>= 3)",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "Encoding": "UTF-8",
  "Date": "2024-12-22",
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  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2025-01-21 04:56:27 UTC",
  "RemoteUrl": "https://github.com/DEploid-dev/DEploid-r",
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  "Packaged": {
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    "User": "root"
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  "Author": "Joe Zhu [aut, cre] (ORCID: <https://orcid.org/0000-0001-7566-2787>),\nJacob Almagro-Garcia [aut],\nGil McVean [aut],\nUniversity of Oxford [cph],\nYinghan Liu [ctb],\nCodeCogs Zyba Ltd [com, cph],\nDeepak Bandyopadhyay [com, cph],\nLutz Kettner [com, cph]",
  "Maintainer": "Joe Zhu <sha.joe.zhu@gmail.com>",
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  "_published": "2026-06-17T10:26:30.871Z",
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    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #83 from DEploid-dev/82_cran_new\n\nclose #82 update",
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    "name": "Joe Zhu",
    "email": "sha.joe.zhu@gmail.com",
    "login": "shajoezhu",
    "orcid": "0000-0001-7566-2787",
    "twitter": "@shajoezhu",
    "description": "Programmer, data scientist, statistician. Made in China, built in NZ, upgraded in Oxford",
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  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "deconvoluting-mixed-genomes",
    "hmm",
    "malaria",
    "mcmc",
    "parasites",
    "phasing",
    "unknown-proportions",
    "zlib",
    "cpp"
  ],
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      "uuid": 3692541
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    "type": "organization",
    "name": "PlasmoGenEpi",
    "followers": 1,
    "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology."
  },
  "_downloads": {
    "count": 259,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DEploid"
  },
  "_devurl": "https://github.com/deploid-dev/deploid-r",
  "_searchresults": 42,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DEploid.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/deploid-dev/deploid-r",
  "_realowner": "deploid-dev",
  "_cranurl": true,
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      "date": "2016-11-25"
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      "date": "2017-07-24"
    },
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      "date": "2017-08-09"
    },
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      "date": "2017-08-09"
    },
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      "date": "2017-09-01"
    },
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      "date": "2018-10-23"
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      "date": "2024-12-23"
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    "dEploid",
    "extractCoverageFromTxt",
    "extractCoverageFromVcf",
    "extractPLAF",
    "haplotypePainter",
    "histWSAF",
    "plotAltVsRef",
    "plotAltVsRefPlotly",
    "plotHistWSAFPlotly",
    "plotObsExpWSAF",
    "plotObsExpWSAFPlotly",
    "plotProportions",
    "plotWSAFvsPLAF",
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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",
      "topics": [
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      ]
    }
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      "author": "Sha Zhu",
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