{
  "_id": "6a169cb4acfb0bcc41d7e8b3",
  "Package": "primerTree",
  "Title": "Visually Assessing the Specificity and Informativeness of Primer\nPairs",
  "Version": "1.1.0",
  "Authors@R": "c(person(given = \"Jim\",\nfamily = \"Hester\",\nrole = \"aut\",\nemail = \"james.hester@gmail.com\"),\nperson(given = \"Matt\",\nfamily = \"Cannon\",\nrole = c(\"aut\", \"cre\"),\nemail = \"matthewvc1@gmail.com\"))",
  "Description": "Identifies potential target sequences for a given set of\nprimers and generates phylogenetic trees annotated with the\ntaxonomies of the predicted amplification products.",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev",
  "Repository": "https://mvesuviusc.r-universe.dev",
  "Date/Publication": "2025-10-28 23:18:37 UTC",
  "RemoteUrl": "https://github.com/mvesuviusc/primertree",
  "RemoteRef": "HEAD",
  "RemoteSha": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-27 07:12:09 UTC",
    "User": "root"
  },
  "Author": "Jim Hester [aut],\nMatt Cannon [aut, cre]",
  "Maintainer": "Matt Cannon <matthewvc1@gmail.com>",
  "MD5sum": "871261c02b5f03066b37c4c317563220",
  "_user": "mvesuviusc",
  "_type": "src",
  "_file": "primerTree_1.1.0.tar.gz",
  "_fileid": "578ec34c457cce62cdb27373165b0e3b57748ead535236e4278c83baf907ac02",
  "_filesize": 295238,
  "_sha256": "578ec34c457cce62cdb27373165b0e3b57748ead535236e4278c83baf907ac02",
  "_created": "2026-05-27T07:12:09.000Z",
  "_published": "2026-05-27T07:26:44.178Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78026145345,
      "time": 137,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7234150227"
    },
    {
      "job": 78026145358,
      "time": 157,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7234155428"
    },
    {
      "job": 78026145333,
      "time": 137,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7234150253"
    },
    {
      "job": 78026145350,
      "time": 141,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7234151749"
    },
    {
      "job": 78026145304,
      "time": 87,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7234359205"
    },
    {
      "job": 78026145384,
      "time": 430,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7234267960"
    },
    {
      "job": 78026145420,
      "time": 173,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7234225359"
    },
    {
      "job": 78026145338,
      "time": 220,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7234202375"
    },
    {
      "job": 78025741765,
      "time": 175,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7234111641"
    },
    {
      "job": 78026145285,
      "time": 146,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7234152053"
    },
    {
      "job": 78026145290,
      "time": 98,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7234139801"
    },
    {
      "job": 78026145360,
      "time": 128,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7234147969"
    },
    {
      "job": 78026145409,
      "time": 109,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7234142759"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/mvesuviusc/primertree",
  "_commit": {
    "id": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
    "author": "MVesuviusC <matthewvc1@gmail.com>",
    "committer": "MVesuviusC <matthewvc1@gmail.com>",
    "message": "Updating version to 1.1.0\n",
    "time": 1761693517
  },
  "_maintainer": {
    "name": "Matt Cannon",
    "email": "matthewvc1@gmail.com",
    "login": "mvesuviusc",
    "bluesky": "@mattvcannon1.bsky.social",
    "description": "",
    "uuid": 5831817
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "directlabels",
      "role": "Depends"
    },
    {
      "package": "gridExtra",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "httr2",
      "role": "Imports"
    },
    {
      "package": "lubridate",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    }
  ],
  "_owner": "mvesuviusc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-38",
      "n": 5
    },
    {
      "week": "2025-44",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v1.1.0",
      "date": "2025-10-28"
    }
  ],
  "_stars": 53,
  "_contributors": [
    {
      "user": "jimhester",
      "count": 75,
      "uuid": 205275
    },
    {
      "user": "mvesuviusc",
      "count": 45,
      "uuid": 5831817
    },
    {
      "user": "infotroph",
      "count": 2,
      "uuid": 1256435
    },
    {
      "user": "omansn",
      "count": 1,
      "uuid": 10858451
    }
  ],
  "_userbio": {
    "uuid": 5831817,
    "type": "user",
    "name": "Matt Cannon"
  },
  "_downloads": {
    "count": 223,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/primerTree"
  },
  "_mentions": 3,
  "_devurl": "https://github.com/mvesuviusc/primertree",
  "_searchresults": 18,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/primerTree.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/mvesuviusc/primertree",
  "_realowner": "mvesuviusc",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2013-10-04"
    },
    {
      "version": "1.0.1",
      "date": "2014-06-09"
    },
    {
      "version": "1.0.3",
      "date": "2016-01-12"
    },
    {
      "version": "1.0.4",
      "date": "2018-12-19"
    },
    {
      "version": "1.0.5",
      "date": "2020-01-24"
    },
    {
      "version": "1.0.6",
      "date": "2022-04-05"
    },
    {
      "version": "1.1.0",
      "date": "2025-10-03"
    }
  ],
  "_exports": [
    "accession2taxid",
    "calc_rank_dist_ave",
    "clustalo",
    "filter_seqs",
    "get_sequence",
    "get_sequences",
    "get_taxonomy",
    "parse_primer_hits",
    "plot_tree",
    "plot_tree_ranks",
    "primer_search",
    "search_primer_pair",
    "seq_lengths",
    "tree_from_alignment"
  ],
  "_datasets": [
    {
      "name": "bryophytes_trnL",
      "title": "PrimerTree results for the bryophyte trnL primers",
      "object": "bryophytes_trnL",
      "class": [
        "primerTree"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mammals_16S",
      "title": "PrimerTree results for the mammalian 16S primers",
      "object": "mammals_16S",
      "class": [
        "primerTree"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "accession2taxid",
      "title": "Maps a nucleotide database accession to a taxonomy database taxId",
      "topics": [
        "accession2taxid"
      ]
    },
    {
      "page": "bryophytes_trnL",
      "title": "PrimerTree results for the bryophyte trnL primers",
      "topics": [
        "bryophytes_trnL"
      ]
    },
    {
      "page": "calc_rank_dist_ave",
      "title": "Summarize pairwise differences.",
      "topics": [
        "calc_rank_dist_ave"
      ]
    },
    {
      "page": "clustalo",
      "title": "Multiple sequence alignment with clustal omega",
      "topics": [
        "clustalo"
      ]
    },
    {
      "page": "filter_seqs",
      "title": "Filter out sequences retrieved by search_primer_pair() that are either too short or too long. The alignment and tree will be recalculated after removing unwanted reads.",
      "topics": [
        "filter_seqs",
        "filter_seqs.primerTree"
      ]
    },
    {
      "page": "get_sequence",
      "title": "Retrieves a fasta sequence from NCBI nucleotide database.",
      "topics": [
        "get_sequence"
      ]
    },
    {
      "page": "get_sequences",
      "title": "Retrieves fasta sequences from NCBI nucleotide database.",
      "topics": [
        "get_sequences"
      ]
    },
    {
      "page": "get_taxonomy",
      "title": "Retrieve the taxonomy information from NCBI for a set of nucleotide gis.",
      "topics": [
        "get_taxonomy"
      ]
    },
    {
      "page": "identify.primerTree_plot",
      "title": "identify the point closest to the mouse click only works on single ranks",
      "topics": [
        "identify.primerTree_plot"
      ]
    },
    {
      "page": "layout_tree_ape",
      "title": "layout a tree using ape, return an object to be plotted by 'plot_tree'",
      "topics": [
        "layout_tree_ape"
      ]
    },
    {
      "page": "mammals_16S",
      "title": "PrimerTree results for the mammalian 16S primers",
      "topics": [
        "mammals_16S"
      ]
    },
    {
      "page": "parse_primer_hits",
      "title": "Parse the primer hits",
      "topics": [
        "parse_primer_hits"
      ]
    },
    {
      "page": "plot_tree",
      "title": "plots a tree, optionally with colored and labeled points by taxonomic rank",
      "topics": [
        "plot_tree"
      ]
    },
    {
      "page": "plot_tree_ranks",
      "title": "plots a tree along with a series of taxonomic ranks",
      "topics": [
        "plot_tree_ranks"
      ]
    },
    {
      "page": "plot.primerTree",
      "title": "plot function for a primerTree object, calls plot_tree_ranks",
      "topics": [
        "plot.primerTree"
      ]
    },
    {
      "page": "primer_search",
      "title": "Query a pair of primers using ncbi's Primer-BLAST, if primers contain iupac",
      "topics": [
        "primer_search"
      ]
    },
    {
      "page": "primerTree",
      "title": "'primerTree' Visually Assessing the Specificity and Informativeness of Primer Pairs",
      "topics": [
        "primerTree-package",
        "primerTree"
      ]
    },
    {
      "page": "search_primer_pair",
      "title": "Automatic primer search Search a given primer pair, retrieving the alignment results, their product sequences, taxonomic information for the sequences, a multiple alignment of the products",
      "topics": [
        "search_primer_pair"
      ]
    },
    {
      "page": "seq_lengths",
      "title": "Get a summary of sequence lengths from a primerTree object",
      "topics": [
        "seq_lengths"
      ]
    },
    {
      "page": "seq_lengths.primerTree",
      "title": "Method for primerTree objects",
      "topics": [
        "seq_lengths.primerTree"
      ]
    },
    {
      "page": "summary.primerTree",
      "title": "Summarize a primerTree result, printing quantiles of sequence length and pairwise differences.",
      "topics": [
        "summary.primerTree"
      ]
    },
    {
      "page": "tree_from_alignment",
      "title": "Construct a neighbor joining tree from a dna alignment",
      "topics": [
        "tree_from_alignment"
      ]
    }
  ],
  "_readme": "https://github.com/mvesuviusc/primertree/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "askpass",
    "cli",
    "codetools",
    "cpp11",
    "curl",
    "digest",
    "directlabels",
    "farver",
    "foreach",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "httr",
    "httr2",
    "isoband",
    "iterators",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "lubridate",
    "magrittr",
    "mime",
    "nlme",
    "openssl",
    "plyr",
    "quadprog",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "timechange",
    "vctrs",
    "viridisLite",
    "withr",
    "XML"
  ],
  "_score": 5.93379088414342,
  "_indexed": true,
  "_nocasepkg": "primertree",
  "_universes": [
    "mvesuviusc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T07:14:17.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "b525a09afcecab42d8419e82bba6552fd8251b89da0ab3eeb1ef602e72449837",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T07:14:24.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "c6bc5489d1fc618d70b576860993bedf72ae5b153fb77a10e40d9fcff1e0c416",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T07:14:19.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "5799a131690f5026b4ecec230f9a0999be46c45b68cc2ee8c2fe083c3253f366",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-27T07:14:22.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "609a039498934f678061ceb5fa373b61882d7f02a729d2422cc359f346f13c32",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T07:26:04.000Z",
      "arch": "aarch64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "c5af6a5db229fc3361093f7f718bb57ebda65f0fae44e803f36fb41dd0881062",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T07:19:51.000Z",
      "arch": "x86_64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "2ba294f6042a8b2c0d8abd539c447d7fb6323c98df4166a4a1a2eb130e2a8962",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T07:18:33.000Z",
      "arch": "aarch64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "c024ecdf4b5f1deebe71860efda0adc0322c31f6b3f5ca8ae1eb2644410a7d51",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-27T07:16:58.000Z",
      "arch": "x86_64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "40422d696fbc8db0891455b04a926c93f3f7c85c42192acb154e6295aea56e98",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-05-27T07:14:57.000Z",
      "arch": "emscripten",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "2b12853e0530e9547ba5de34430b0bbf92e7c4a18a3f47ad6190131c35c8ffc7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T07:13:31.000Z",
      "arch": "x86_64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "648eb60368eb3e4e3ae94ce226a158436906b41fe1ca0fdff6f0a1cc15443413",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T07:13:47.000Z",
      "arch": "x86_64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "8a135499da19508744eb6dba0366762784846f569dfd3af2b1fabd2430da1a9e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-27T07:13:32.000Z",
      "arch": "x86_64",
      "commit": "3df2a16c1d0fae50bdda43fdc78880b512f2e7a5",
      "fileid": "40c6ef861f64274af98bbccb4d4be812ee7b6f95bd76f63e7092f67c76be1662",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mvesuviusc/actions/runs/26496445854"
    }
  ]
}