{
  "_id": "6a60803b14e95619b75da7f1",
  "Type": "Package",
  "Package": "rprimer",
  "Title": "Design Degenerate Oligos from a Multiple DNA Sequence Alignment",
  "Version": "1.17.0",
  "Description": "Functions, workflow, and a Shiny application for\nvisualizing sequence conservation and designing degenerate\nprimers, probes, and (RT)-(q/d)PCR assays from a multiple DNA\nsequence alignment. The results can be presented in data frame\nformat and visualized as dashboard-like plots. For more\ninformation, please see the package vignette.",
  "Authors@R": "person(given = \"Sofia\",\nfamily = \"Persson\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sofiapersson27@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2611-3030\"))",
  "License": "GPL-3",
  "URL": "https://github.com/sofpn/rprimer",
  "BugReports": "https://github.com/sofpn/rprimer/issues",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.2",
  "RdMacros": "mathjaxr",
  "biocViews": "Alignment, ddPCR, Coverage, MultipleSequenceAlignment,\nSequenceMatching, qPCR",
  "biocType": "Software",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:31 UTC",
  "RemoteUrl": "https://github.com/bioc/rprimer",
  "RemoteRef": "HEAD",
  "RemoteSha": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-22 08:26:27 UTC",
    "User": "root"
  },
  "Author": "Sofia Persson [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-2611-3030>)",
  "Maintainer": "Sofia Persson <sofiapersson27@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "rprimer_1.17.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/a69c2bb667dfc50beb365107e07f86c898aaae03d1c5490e4340dd96ef288806",
  "_filesize": 854951,
  "_sha256": "a69c2bb667dfc50beb365107e07f86c898aaae03d1c5490e4340dd96ef288806",
  "_expires": "2026-10-30T08:32:57.000Z",
  "_created": "2026-07-22T08:26:27.000Z",
  "_published": "2026-07-22T08:32:59.761Z",
  "_bioccheck": {
    "error": 0,
    "warning": 3,
    "note": 5
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462",
  "_status": "failure",
  "_upstream": "https://github.com/bioc/rprimer",
  "_commit": {
    "id": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381051
  },
  "_maintainer": {
    "name": "Sofia Persson",
    "email": "sofiapersson27@gmail.com",
    "login": "sofiapers",
    "description": "",
    "uuid": 151018550,
    "orcid": "0000-0003-2611-3030"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 88871092694,
      "time": 185,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8523131393"
    },
    {
      "job": 88871092776,
      "time": 340,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8523196536"
    },
    {
      "job": 88871092697,
      "time": 237,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8523152891"
    },
    {
      "job": 88871092747,
      "time": 132,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8523109184"
    },
    {
      "job": 88871092739,
      "time": 202,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8523137963"
    },
    {
      "job": 88870017480,
      "time": 304,
      "config": "source",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8523052514"
    },
    {
      "job": 88871092705,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8523128763"
    },
    {
      "job": 88871092718,
      "time": 169,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8523124558"
    },
    {
      "job": 88871092804,
      "time": 202,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "8523139765"
    },
    {
      "job": 88871092734,
      "time": 198,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8523136284"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "bslib",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "mathjaxr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinycssloaders",
      "role": "Imports"
    },
    {
      "package": "shinyFeedback",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "styler",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.16.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "alignment",
    "ddpcr",
    "coverage",
    "multiplesequencealignment",
    "sequencematching",
    "qpcr"
  ],
  "_stars": 4,
  "_contributors": [
    {
      "user": "sofpn",
      "count": 379,
      "uuid": 39567760
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    },
    {
      "user": "petehaitch",
      "count": 3,
      "uuid": 1049741
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 450,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 394,
    "source": "https://www.bioconductor.org/packages/stats/bioc/rprimer"
  },
  "_devurl": "https://github.com/sofpn/rprimer",
  "_searchresults": 16,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/rprimer.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/sofpn/rprimer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "checkMatch",
    "consensusProfile",
    "designAssays",
    "designOligos",
    "plotData",
    "RprimerAssay",
    "RprimerMatchAssay",
    "RprimerMatchOligo",
    "RprimerOligo",
    "RprimerProfile",
    "runRprimerApp"
  ],
  "_datasets": [
    {
      "name": "exampleRprimerAlignment",
      "title": "Example datasets",
      "object": "exampleRprimerAlignment",
      "file": "exampleRprimerAlignment.RData",
      "class": [
        "DNAMultipleAlignment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exampleRprimerAssay",
      "title": "Example datasets",
      "object": "exampleRprimerAssay",
      "file": "exampleRprimerAssay.RData",
      "class": [
        "RprimerAssay"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exampleRprimerMatchAssay",
      "title": "Example datasets",
      "object": "exampleRprimerMatchAssay",
      "file": "exampleRprimerMatchAssay.RData",
      "class": [
        "RprimerMatchAssay"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exampleRprimerMatchOligo",
      "title": "Example datasets",
      "object": "exampleRprimerMatchOligo",
      "file": "exampleRprimerMatchOligo.RData",
      "class": [
        "RprimerMatchOligo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exampleRprimerOligo",
      "title": "Example datasets",
      "object": "exampleRprimerOligo",
      "file": "exampleRprimerOligo.RData",
      "class": [
        "RprimerOligo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exampleRprimerProfile",
      "title": "Example datasets",
      "object": "exampleRprimerProfile",
      "file": "exampleRprimerProfile.RData",
      "class": [
        "RprimerProfile"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "checkMatch",
      "title": "Check how oligos and assays match to their target sequences",
      "topics": [
        "checkMatch",
        "checkMatch,RprimerAssay-method",
        "checkMatch,RprimerOligo-method"
      ]
    },
    {
      "page": "consensusProfile",
      "title": "Get sequence information from an alignment",
      "topics": [
        "consensusProfile"
      ]
    },
    {
      "page": "designAssays",
      "title": "Design (RT)-PCR assays",
      "topics": [
        "designAssays"
      ]
    },
    {
      "page": "designOligos",
      "title": "Design primers and probes",
      "topics": [
        "designOligos"
      ]
    },
    {
      "page": "example-datasets",
      "title": "Example datasets",
      "topics": [
        "example-datasets",
        "exampleRprimerAlignment",
        "exampleRprimerAssay",
        "exampleRprimerMatchAssay",
        "exampleRprimerMatchOligo",
        "exampleRprimerOligo",
        "exampleRprimerProfile"
      ]
    },
    {
      "page": "plotData",
      "title": "Plot an Rprimer object",
      "topics": [
        "plotData",
        "plotData,RprimerAssay-method",
        "plotData,RprimerMatchAssay-method",
        "plotData,RprimerMatchOligo-method",
        "plotData,RprimerOligo-method",
        "plotData,RprimerProfile-method"
      ]
    },
    {
      "page": "Rprimer-classes",
      "title": "S4 classes for representation of different Rprimer objects",
      "topics": [
        ".RprimerAssay",
        ".RprimerMatchAssay",
        ".RprimerMatchOligo",
        ".RprimerOligo",
        ".RprimerProfile",
        "coerce",
        "Rprimer-classes",
        "RprimerAssay",
        "RprimerAssay-class",
        "RprimerMatchAssay",
        "RprimerMatchAssay-class",
        "RprimerMatchOligo",
        "RprimerMatchOligo-class",
        "RprimerOligo",
        "RprimerOligo-class",
        "RprimerProfile",
        "RprimerProfile-class"
      ]
    },
    {
      "page": "runRprimerApp",
      "title": "rprimer Shiny application",
      "topics": [
        "runRprimerApp"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/rprimer/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "BiocGenerics",
    "Biostrings",
    "bslib",
    "cachem",
    "cli",
    "commonmark",
    "cpp11",
    "crayon",
    "crosstalk",
    "digest",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "mathjaxr",
    "memoise",
    "mime",
    "otel",
    "patchwork",
    "plyr",
    "promises",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "rmarkdown",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "shinycssloaders",
    "shinyFeedback",
    "sourcetools",
    "stringi",
    "stringr",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_score": 4.28330122870355,
  "_indexed": true,
  "_nocasepkg": "rprimer",
  "_universes": [
    "bioc",
    "sofiapers",
    "sofpn"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-07-22T08:30:46.000Z",
      "distro": "resolute",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/644d08ecb8ac8ac26b4005a9786eaaf1dca19af2aa6e389b361aed964d420da4",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-07-22T08:29:25.000Z",
      "distro": "resolute",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/a0ef4459d1eac6617b7050717a5012a9e3e4ffd13f6bf8b64a852edefcaceb2c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-07-22T08:28:11.000Z",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/b1016c6f6bf8ec5ac221f91c33d4252f1c72b7e376b5a53e2ff7ede17a874135",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-07-22T08:28:26.000Z",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/af62358dad0de7f41cbbfedda02f1a02bbbfe512bd0bec679de614cc1bdd469d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.17.0",
      "date": "2026-07-22T08:29:54.000Z",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/ff0cfd605195619babede970af4db77769f60356fac05e9dd1a1150645e33a1d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-07-22T08:28:05.000Z",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/b23ef8b6f6612cb8a429caa382acb23a2ec0f9d065143482ed7be24257d28452",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-07-22T08:28:29.000Z",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/2f6f6cd7a61729f923ec0e8400e81cd49912133fdf6c9f14098e21436c334ac3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-07-22T08:28:11.000Z",
      "commit": "beb25279f6f52c4ffe52a9b5f1469933f8055ea7",
      "fileid": "https://r2.ropensci.org/89537488e57d157874f1270c94e647fd1f4c0ae6f84fbe81ec7bd5591a631520",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29903674462"
    }
  ]
}