{
  "_id": "6a104604acfb0bcc41c9e998",
  "Package": "amplify",
  "Title": "Automate PCR Tasks Reproducibly",
  "Version": "0.1.0",
  "Authors@R": "person(given = \"Kai\",\nfamily = \"Aragaki\",\nrole = c(\"aut\", \"cre\"),\nemail = \"adamaragaki@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9458-0426\"))",
  "Description": "PCR tasks - like plate layout planning, dilution\ncalculations, visualization, and analysis - are often\nrepetitive, tedious, prone to error, and poorly documented.\namplify seeks to automate these tasks, as well as documenting\nthem (through both code and generated reports) as a bonus.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Remotes": [
    "KaiAragaki/gplate",
    "KaiAragaki/mop"
  ],
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "URL": "https://kaiaragaki.github.io/amplify/",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev libnode-dev libx11-dev",
  "Repository": "https://kaiaragaki.r-universe.dev",
  "Date/Publication": "2024-10-05 23:42:52 UTC",
  "RemoteUrl": "https://github.com/KaiAragaki/amplify",
  "RemoteRef": "HEAD",
  "RemoteSha": "d3bb78428ff1b437652b2289d2402a063840787b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-11 05:39:19 UTC",
    "User": "root"
  },
  "Author": "Kai Aragaki [aut, cre] (ORCID: <https://orcid.org/0000-0002-9458-0426>)",
  "Maintainer": "Kai Aragaki <adamaragaki@gmail.com>",
  "MD5sum": "13f803155c407f466715fe7aaa7011e3",
  "_user": "kaiaragaki",
  "_type": "src",
  "_file": "amplify_0.1.0.tar.gz",
  "_fileid": "8fe28c12af35c1dce55d438135bcbccf2296650c60f4e7632761aa03f4ffffce",
  "_filesize": 1539808,
  "_sha256": "8fe28c12af35c1dce55d438135bcbccf2296650c60f4e7632761aa03f4ffffce",
  "_created": "2026-05-11T05:39:19.000Z",
  "_published": "2026-05-22T12:03:16.554Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77375490745,
      "time": 123,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77375491040,
      "time": 139,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77375490836,
      "time": 70,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77375490880,
      "time": 86,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77375490011,
      "time": 254,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "6911071753"
    },
    {
      "job": 77375490187,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7160008357"
    },
    {
      "job": 77375491036,
      "time": 83,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77375490960,
      "time": 62,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 77375490999,
      "time": 90,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_buildurl": "https://github.com/r-universe/kaiaragaki/actions/runs/25544835650",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/KaiAragaki/amplify",
  "_commit": {
    "id": "d3bb78428ff1b437652b2289d2402a063840787b",
    "author": "Kai Aragaki <kaiaragaki@proton.me>",
    "committer": "Kai Aragaki <kaiaragaki@proton.me>",
    "message": "pcr_lib_calc: do not return a grouped dataframe\n",
    "time": 1728171772
  },
  "_maintainer": {
    "name": "Kai Aragaki",
    "email": "adamaragaki@gmail.com",
    "orcid": "0000-0002-9458-0426"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.1.0",
      "role": "Imports"
    },
    {
      "package": "forcats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "gplate",
      "role": "Imports"
    },
    {
      "package": "gt",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "mop",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "readxl",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "vctrs",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "kaiaragaki",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "kaiaragaki",
      "count": 16,
      "uuid": 7370516
    }
  ],
  "_userbio": {
    "uuid": 7370516,
    "type": "user",
    "name": "Kai Aragaki",
    "description": "whatever the exact opposite of an emotional support dog is"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/amplify"
  },
  "_devurl": "https://github.com/kaiaragaki/amplify",
  "_pkgdown": "https://kaiaragaki.github.io/amplify/",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/amplify.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "as_pcr",
    "pcr_calc_slope",
    "pcr_control",
    "pcr_lib_calc",
    "pcr_lib_qc",
    "pcr_lib_qc_plot_conc",
    "pcr_lib_qc_plot_dil",
    "pcr_lib_qc_plot_outliers",
    "pcr_lib_qc_plot_slope",
    "pcr_lib_qc_report",
    "pcr_plan",
    "pcr_plan_report",
    "pcr_plate_view",
    "pcr_plot",
    "pcr_rq",
    "read_pcr",
    "scrub",
    "tidy_lab",
    "well_data"
  ],
  "_datasets": [
    {
      "name": "dummy_rna_conc",
      "title": "Example data of RNA samples with concentrations",
      "object": "dummy_rna_conc",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sample",
        "conc"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dummy_rna_conc",
      "title": "Example data of RNA samples with concentrations",
      "topics": [
        "dummy_rna_conc"
      ]
    },
    {
      "page": "pcr_calc_slope",
      "title": "Recalcuate standard slope of quantity vs Ct",
      "topics": [
        "pcr_calc_slope"
      ]
    },
    {
      "page": "pcr_control",
      "title": "Calculate Delta Ct mean based on given control probe",
      "topics": [
        "pcr_control",
        "pcr_control.data.frame",
        "pcr_control.pcr"
      ]
    },
    {
      "page": "pcr_lib_calc",
      "title": "Calculate library PCR concentrations",
      "topics": [
        "pcr_lib_calc"
      ]
    },
    {
      "page": "pcr_lib_qc",
      "title": "Create library prep quality control data",
      "topics": [
        "pcr_lib_qc"
      ]
    },
    {
      "page": "pcr_lib_qc_plot_conc",
      "title": "Plot concentration of libraries across samples",
      "topics": [
        "pcr_lib_qc_plot_conc"
      ]
    },
    {
      "page": "pcr_lib_qc_plot_dil",
      "title": "Plot standard dilutions compared to a perfect dilution",
      "topics": [
        "pcr_lib_qc_plot_dil"
      ]
    },
    {
      "page": "pcr_lib_qc_plot_outliers",
      "title": "Plot mean centered samples without putative outliers",
      "topics": [
        "pcr_lib_qc_plot_outliers"
      ]
    },
    {
      "page": "pcr_lib_qc_plot_slope",
      "title": "Plot the log of library quantities vs Ct",
      "topics": [
        "pcr_lib_qc_plot_slope"
      ]
    },
    {
      "page": "pcr_lib_qc_report",
      "title": "Generate visual library prep pcr quality control report",
      "topics": [
        "pcr_lib_qc_report"
      ]
    },
    {
      "page": "pcr_plan",
      "title": "Plan PCR experiment",
      "topics": [
        "pcr_plan"
      ]
    },
    {
      "page": "pcr_plan_report",
      "title": "Create a report from a PCR plan",
      "topics": [
        "pcr_plan_report"
      ]
    },
    {
      "page": "pcr_plate_view",
      "title": "View sample plating layout",
      "topics": [
        "pcr_plate_view"
      ]
    },
    {
      "page": "pcr_plot",
      "title": "Plot qPCR results",
      "topics": [
        "pcr_plot",
        "pcr_plot.data.frame",
        "pcr_plot.pcr"
      ]
    },
    {
      "page": "pcr_rq",
      "title": "Recalculate relative quantities for a given experiment",
      "topics": [
        "pcr_rq",
        "pcr_rq.data.frame",
        "pcr_rq.pcr"
      ]
    }
  ],
  "_pkglogo": "https://github.com/KaiAragaki/amplify/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/KaiAragaki/amplify/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "bigD",
    "bitops",
    "bslib",
    "cachem",
    "cellranger",
    "cli",
    "codetools",
    "commonmark",
    "cpp11",
    "crayon",
    "curl",
    "digest",
    "doSNOW",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "forcats",
    "foreach",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gplate",
    "gt",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "juicyjuice",
    "knitr",
    "labeling",
    "lifecycle",
    "litedown",
    "magrittr",
    "markdown",
    "memoise",
    "mime",
    "mop",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reactable",
    "reactR",
    "readxl",
    "rematch",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "snow",
    "stringi",
    "stringr",
    "terra",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "V8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xml2",
    "yaml"
  ],
  "_score": 1.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "amplify",
  "_universes": [
    "kaiaragaki"
  ],
  "_binaries": [
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-05-08T08:16:01.000Z",
      "distro": "noble",
      "commit": "d3bb78428ff1b437652b2289d2402a063840787b",
      "fileid": "44727446fc18054aafba42bf25a9868916140c597a78f35480c3e257d370dfda",
      "status": "failure",
      "buildurl": "https://github.com/r-universe/kaiaragaki/actions/runs/25544835650"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-05-22T12:02:58.000Z",
      "commit": "d3bb78428ff1b437652b2289d2402a063840787b",
      "fileid": "9eacc0051fca7ffb033db70327d8d4ffca44fbec2741368cd2a55a76f6754c95",
      "status": "success",
      "buildurl": "https://github.com/r-universe/kaiaragaki/actions/runs/25544835650"
    }
  ]
}