{
  "_id": "6a1f0601b401979e7341bac8",
  "Package": "DEploid",
  "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",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://plasmogenepi.r-universe.dev",
  "Date/Publication": "2025-01-21 04:56:27 UTC",
  "RemoteUrl": "https://github.com/DEploid-dev/DEploid-r",
  "RemoteRef": "HEAD",
  "RemoteSha": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-18 07:12:44 UTC",
    "User": "root"
  },
  "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>",
  "MD5sum": "f652c3722a8162b1e686a0b5b89ce3a1",
  "_user": "plasmogenepi",
  "_type": "src",
  "_file": "DEploid_0.5.7.tar.gz",
  "_fileid": "1ed82b6236112fc3c0e01e777e343a1a1393b7b81b43b2dd0975b30365026cda",
  "_filesize": 1208328,
  "_sha256": "1ed82b6236112fc3c0e01e777e343a1a1393b7b81b43b2dd0975b30365026cda",
  "_created": "2026-05-18T07:12:44.000Z",
  "_published": "2026-06-02T16:34:09.387Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79121506181,
      "time": 197,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051615144"
    },
    {
      "job": 79121506075,
      "time": 197,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051615452"
    },
    {
      "job": 79121506855,
      "time": 188,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051612495"
    },
    {
      "job": 79121506633,
      "time": 159,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051604853"
    },
    {
      "job": 79121506517,
      "time": 117,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051648795"
    },
    {
      "job": 79121507014,
      "time": 290,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051681734"
    },
    {
      "job": 79121506524,
      "time": 164,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051674790"
    },
    {
      "job": 79121506178,
      "time": 289,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051661486"
    },
    {
      "job": 79121505743,
      "time": 290,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051559670"
    },
    {
      "job": 79121505427,
      "time": 149,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7363884280"
    },
    {
      "job": 79121506036,
      "time": 191,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051613764"
    },
    {
      "job": 79121507143,
      "time": 213,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051619365"
    },
    {
      "job": 79121506883,
      "time": 221,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051621785"
    }
  ],
  "_buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/DEploid-dev/DEploid-r",
  "_commit": {
    "id": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
    "author": "Joe Zhu <sha.joe.zhu@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #83 from DEploid-dev/82_cran_new\n\nclose #82 update",
    "time": 1737435387
  },
  "_maintainer": {
    "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",
    "uuid": 3692541
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.0",
      "role": "Depends"
    },
    {
      "package": "DEploid.utils",
      "version": ">= 0.0.1",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.11.2",
      "role": "Imports"
    },
    {
      "package": "scales",
      "version": ">= 0.4.0",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "version": ">= 4.7.1",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "version": ">= 1.5",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "version": ">= 1.6",
      "role": "Imports"
    },
    {
      "package": "htmlwidgets",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 0.9.0",
      "role": "Suggests"
    }
  ],
  "_owner": "deploid-dev",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "deconvoluting-mixed-genomes",
    "hmm",
    "malaria",
    "mcmc",
    "parasites",
    "phasing",
    "unknown-proportions",
    "zlib",
    "cpp"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "shajoezhu",
      "count": 254,
      "uuid": 3692541
    },
    {
      "user": "liuyingh",
      "count": 13,
      "uuid": 29950721
    }
  ],
  "_userbio": {
    "uuid": 140542976,
    "type": "organization",
    "name": "PlasmoGenEpi",
    "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology."
  },
  "_downloads": {
    "count": 175,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DEploid"
  },
  "_devurl": "https://github.com/deploid-dev/deploid-r",
  "_searchresults": 41,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "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,
  "_releases": [
    {
      "version": "0.3.2",
      "date": "2016-11-25"
    },
    {
      "version": "0.4.1",
      "date": "2017-07-24"
    },
    {
      "version": "0.4.2",
      "date": "2017-08-09"
    },
    {
      "version": "0.4.3",
      "date": "2017-08-09"
    },
    {
      "version": "0.4.4",
      "date": "2017-09-01"
    },
    {
      "version": "0.5.0",
      "date": "2018-05-18"
    },
    {
      "version": "0.5.1",
      "date": "2018-10-21"
    },
    {
      "version": "0.5.2",
      "date": "2018-10-23"
    },
    {
      "version": "0.5.3",
      "date": "2020-04-21"
    },
    {
      "version": "0.5.4",
      "date": "2024-10-14"
    },
    {
      "version": "0.5.6",
      "date": "2024-12-23"
    },
    {
      "version": "0.5.7",
      "date": "2025-01-20"
    }
  ],
  "_exports": [
    "computeObsWSAF",
    "dEploid",
    "extractCoverageFromTxt",
    "extractCoverageFromVcf",
    "extractPLAF",
    "haplotypePainter",
    "histWSAF",
    "plotAltVsRef",
    "plotAltVsRefPlotly",
    "plotHistWSAFPlotly",
    "plotObsExpWSAF",
    "plotObsExpWSAFPlotly",
    "plotProportions",
    "plotWSAFvsPLAF",
    "plotWSAFVsPLAFPlotly"
  ],
  "_help": [
    {
      "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": [
        "plotWSAFVsPLAFPlotly"
      ]
    }
  ],
  "_readme": "https://github.com/DEploid-dev/DEploid-r/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "combinat",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "DEploid.utils",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libz",
      "package": "zlib1g",
      "headers": "zlib1g-dev",
      "source": "zlib",
      "version": "1:1.3.dfsg-3.1ubuntu2.1",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "dEploid-Arguments.Rmd",
      "filename": "dEploid-Arguments.html",
      "title": "Command Line Arguments",
      "author": "Sha Zhu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Mostly used",
        "You may also try",
        "Example",
        "Reporting Bugs",
        "Citing DEploid"
      ],
      "created": "2016-10-30 16:27:48",
      "modified": "2024-12-20 04:02:44",
      "commits": 7
    }
  ],
  "_score": 4.311753861055754,
  "_indexed": false,
  "_nocasepkg": "deploid",
  "_universes": [
    "plasmogenepi"
  ],
  "_indexurl": "https://deploid-dev.r-universe.dev/DEploid",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.5.7",
      "date": "2026-05-18T07:15:55.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "84358e718a3d307ebac95a338bce4991a8404c1c3a1245bd5708bee148a4b101",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.5.7",
      "date": "2026-05-18T07:15:46.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "9ef3f315977d011093a749ba553246960cf419708c3593e655d011ca6e33239a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.5.7",
      "date": "2026-05-18T07:15:45.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "0496cb52ea4c9fdf392648086640eb7ebc0f9092355afabde94394fb4b2cecd4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.5.7",
      "date": "2026-05-18T07:15:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "cb229b02e22b4d9d61b223fa2bf68f289246fdd891ae09d749c47c773e4076f2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.5.7",
      "date": "2026-05-18T07:18:10.000Z",
      "arch": "aarch64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "6da34b6800ef2f6ee965d0c6b9435fef903a7a3d4121049ff45d0b09e6f4b0e1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.5.7",
      "date": "2026-05-18T07:19:02.000Z",
      "arch": "x86_64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "1d000d16d520fefc063cb406a7045b09af3f36e417f7ccb8b590388f3dee3123",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.5.7",
      "date": "2026-05-18T07:19:20.000Z",
      "arch": "aarch64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "9d6f5205069115841ee690970df29f805e9b9558edb132c4d45606897931f4ae",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.5.7",
      "date": "2026-05-18T07:17:47.000Z",
      "arch": "x86_64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "46eeca4c2e0c6a2130827e610ab4945368a9fa18e7af19a3522c7cf4cc7f115f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.5.7",
      "date": "2026-05-18T07:14:34.000Z",
      "arch": "x86_64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "22539eeac64c34985ce03aadcc156e0cb67f2f7e4a1693981ea5ca67d0131c7f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.5.7",
      "date": "2026-05-18T07:14:44.000Z",
      "arch": "x86_64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "18f2b4571bfa6fc4151cf18b0160b4667223dca2e2ae0a536eb1d13cef7a3e6f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.5.7",
      "date": "2026-05-18T07:14:42.000Z",
      "arch": "x86_64",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "320fb92aba4ceb9cee6a701111d09a2f8044e33f2c6f90e538b23669456ee19b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.5.7",
      "date": "2026-06-02T16:33:21.000Z",
      "arch": "emscripten",
      "commit": "13f0fe1299511645d21e4c2558e85602c6cfc0f9",
      "fileid": "e2c620e6bdca6fa17d10c7771a5ac319d6e3069d022079f3a02d77d8bc0b5726",
      "status": "success",
      "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/26018822066"
    }
  ]
}