{
  "_id": "6a2284e8cd65a98ecbd52d03",
  "Package": "microseq",
  "Type": "Package",
  "Title": "Basic Biological Sequence Handling",
  "Version": "2.1.8",
  "Date": "2025-10-08",
  "Authors@R": "c(person(given = \"Lars\",\nfamily = \"Snipen\",\nrole = c(\"aut\", \"cre\"),\nemail = \"lars.snipen@nmbu.no\"),\nperson(given = c(\"Kristian\", \"Hovde\"),\nfamily = \"Liland\",\nrole = \"aut\"))",
  "Maintainer": "Lars Snipen <lars.snipen@nmbu.no>",
  "Description": "Basic functions for microbial sequence data analysis. The\nidea is to use generic R data structures as much as possible,\nmaking R data wrangling possible also for sequence data.",
  "License": "GPL-2",
  "ZipData": "TRUE",
  "URL": "https://github.com/larssnip/microseq",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://larssnip.r-universe.dev",
  "Date/Publication": "2025-10-08 12:55:46 UTC",
  "RemoteUrl": "https://github.com/larssnip/microseq",
  "RemoteRef": "HEAD",
  "RemoteSha": "68b48e6704780019127f358aa2cfbb2424e231ea",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-05 08:04:13 UTC",
    "User": "root"
  },
  "Author": "Lars Snipen [aut, cre],\nKristian Hovde Liland [aut]",
  "MD5sum": "429dfe4e2a8b48729dc29439935fe0e0",
  "_user": "larssnip",
  "_type": "src",
  "_file": "microseq_2.1.8.tar.gz",
  "_fileid": "0bf95992e67cf160385c4eb1646ed693c95fc4dfa037f39ccf894b28f7ccf894",
  "_filesize": 235205,
  "_sha256": "0bf95992e67cf160385c4eb1646ed693c95fc4dfa037f39ccf894b28f7ccf894",
  "_created": "2026-06-05T08:04:13.000Z",
  "_published": "2026-06-05T08:12:24.538Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79688542444,
      "time": 123,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7431797961"
    },
    {
      "job": 79688542423,
      "time": 132,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7431799984"
    },
    {
      "job": 79688542381,
      "time": 128,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7431799744"
    },
    {
      "job": 79688542430,
      "time": 128,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7431798844"
    },
    {
      "job": 79688542533,
      "time": 183,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7431806035"
    },
    {
      "job": 79688542440,
      "time": 443,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7431877479"
    },
    {
      "job": 79688542338,
      "time": 163,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7431798753"
    },
    {
      "job": 79688542374,
      "time": 295,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7431839891"
    },
    {
      "job": 79688200209,
      "time": 142,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7431760231"
    },
    {
      "job": 79688542406,
      "time": 109,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7431793075"
    },
    {
      "job": 79688542361,
      "time": 117,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7431795339"
    },
    {
      "job": 79688542359,
      "time": 109,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7431792747"
    },
    {
      "job": 79688542419,
      "time": 122,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7431797119"
    }
  ],
  "_buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/larssnip/microseq",
  "_commit": {
    "id": "68b48e6704780019127f358aa2cfbb2424e231ea",
    "author": "Lars-Gustav Snipen <lars.snipen@nmbu.no>",
    "committer": "Lars-Gustav Snipen <lars.snipen@nmbu.no>",
    "message": "Fixed small bug in readFasta and readFastq to not be mislead by tabs in the Header lines\n",
    "time": 1759928146
  },
  "_maintainer": {
    "name": "Lars Snipen",
    "email": "lars.snipen@nmbu.no",
    "login": "larssnip",
    "description": "",
    "uuid": 13868182
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "tibble",
      "role": "Depends"
    },
    {
      "package": "stringr",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Depends"
    },
    {
      "package": "rlang",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.9.8",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Suggests"
    }
  ],
  "_owner": "larssnip",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-29",
      "n": 1
    },
    {
      "week": "2025-38",
      "n": 3
    },
    {
      "week": "2025-41",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "larssnip",
      "count": 56,
      "uuid": 13868182
    },
    {
      "user": "khliland",
      "count": 1,
      "uuid": 9257806
    },
    {
      "user": "michaelchirico",
      "count": 1,
      "uuid": 7606389
    }
  ],
  "_userbio": {
    "uuid": 13868182,
    "type": "user",
    "name": "Lars Snipen"
  },
  "_downloads": {
    "count": 503,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/microseq"
  },
  "_devurl": "https://github.com/larssnip/microseq",
  "_searchresults": 97,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/microseq.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/larssnip/microseq",
  "_realowner": "larssnip",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2016-07-26"
    },
    {
      "version": "1.2",
      "date": "2017-01-13"
    },
    {
      "version": "1.2.1",
      "date": "2018-02-07"
    },
    {
      "version": "1.2.2",
      "date": "2018-02-12"
    },
    {
      "version": "1.2.3",
      "date": "2019-07-11"
    },
    {
      "version": "1.3",
      "date": "2019-10-27"
    },
    {
      "version": "2.0",
      "date": "2020-01-09"
    },
    {
      "version": "2.1",
      "date": "2020-05-29"
    },
    {
      "version": "2.1.1",
      "date": "2020-06-04"
    },
    {
      "version": "2.1.2",
      "date": "2020-07-05"
    },
    {
      "version": "2.1.4",
      "date": "2021-01-25"
    },
    {
      "version": "2.1.5",
      "date": "2021-10-30"
    },
    {
      "version": "2.1.6",
      "date": "2023-08-21"
    },
    {
      "version": "2.1.7",
      "date": "2025-09-18"
    }
  ],
  "_exports": [
    "backTranslate",
    "findGenes",
    "findOrfs",
    "findrRNA",
    "gff2fasta",
    "gregexpr",
    "iupac2regex",
    "lorfs",
    "msa2mat",
    "msalign",
    "msaTrim",
    "muscle",
    "orfLength",
    "orfSignature",
    "readFasta",
    "readFastq",
    "readGFF",
    "regex2iupac",
    "reverseComplement",
    "translate",
    "writeFasta",
    "writeFastq",
    "writeGFF"
  ],
  "_help": [
    {
      "page": "backTranslate",
      "title": "Replace amino acids with codons",
      "topics": [
        "backTranslate"
      ]
    },
    {
      "page": "findGenes",
      "title": "Finding coding genes",
      "topics": [
        "findGenes"
      ]
    },
    {
      "page": "findOrfs",
      "title": "Finding ORFs in genomes",
      "topics": [
        "findOrfs"
      ]
    },
    {
      "page": "findrRNA",
      "title": "Finding rRNA genes",
      "topics": [
        "findrRNA"
      ]
    },
    {
      "page": "gff2fasta",
      "title": "Retrieving annotated sequences",
      "topics": [
        "gff2fasta"
      ]
    },
    {
      "page": "gregexpr",
      "title": "Extended 'gregexpr' with substring retrieval",
      "topics": [
        "gregexpr"
      ]
    },
    {
      "page": "iupac2regex",
      "title": "Ambiguity symbol conversion",
      "topics": [
        "iupac2regex",
        "regex2iupac"
      ]
    },
    {
      "page": "lorfs",
      "title": "Longest ORF",
      "topics": [
        "lorfs"
      ]
    },
    {
      "page": "microseq",
      "title": "Basic Biological Sequence Analysis",
      "topics": [
        "microseq"
      ]
    },
    {
      "page": "msa2mat",
      "title": "Convert alignment to matrix",
      "topics": [
        "msa2mat"
      ]
    },
    {
      "page": "msalign",
      "title": "Multiple alignment",
      "topics": [
        "msalign"
      ]
    },
    {
      "page": "msaTrim",
      "title": "Trimming multiple sequence alignments",
      "topics": [
        "msaTrim"
      ]
    },
    {
      "page": "muscle",
      "title": "Multiple alignment using MUSCLE",
      "topics": [
        "muscle"
      ]
    },
    {
      "page": "orfLength",
      "title": "Length of ORF",
      "topics": [
        "orfLength"
      ]
    },
    {
      "page": "orfSignature",
      "title": "Signature for each ORF",
      "topics": [
        "orfSignature"
      ]
    },
    {
      "page": "readFasta",
      "title": "Read and write FASTA files",
      "topics": [
        "readFasta",
        "writeFasta"
      ]
    },
    {
      "page": "readFastq",
      "title": "Read and write FASTQ files",
      "topics": [
        "readFastq",
        "writeFastq"
      ]
    },
    {
      "page": "readGFF",
      "title": "Reading and writing GFF-tables",
      "topics": [
        "readGFF",
        "writeGFF"
      ]
    },
    {
      "page": "reverseComplement",
      "title": "Reverse-complementation of DNA",
      "topics": [
        "reverseComplement"
      ]
    },
    {
      "page": "translate",
      "title": "Translation according to the standard genetic code",
      "topics": [
        "translate"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "data.table",
    "dplyr",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "R6",
    "Rcpp",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_sysdeps": [
    {
      "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"
    }
  ],
  "_score": 5.020195489753195,
  "_indexed": true,
  "_nocasepkg": "microseq",
  "_universes": [
    "larssnip"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.8",
      "date": "2026-06-05T08:06:19.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "9962c881013ff60a11c222f05f941ea50f2bffaa7ef60f0ec385d71c7d21369e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.8",
      "date": "2026-06-05T08:06:23.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "10762f43b5454a965e965bed9e329143e21b37ccc2e8a18cd8849e2f99870776",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.8",
      "date": "2026-06-05T08:06:25.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "3024088cd364c21b8d0e4d93c53433cb7870293e536bc64221b6340396514e84",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.8",
      "date": "2026-06-05T08:06:19.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "35dadaab8ccf6cbc79527adbde0ce2f9b16beda53a3a450e330187a8f0bb3119",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.8",
      "date": "2026-06-05T08:06:42.000Z",
      "arch": "aarch64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "29a6e3895fb63fad758ec105231393881fb5ca618a553c3ecc453d50f4f11f57",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.8",
      "date": "2026-06-05T08:10:08.000Z",
      "arch": "x86_64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "19eb8c2431d06c721c6a72bc103f8a56ae9325de40e1d029bbc8fae99ed130d4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.8",
      "date": "2026-06-05T08:06:16.000Z",
      "arch": "aarch64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "6312cdda23d01234801e2c14b6beae904698ee8e18453aeb4297842c06c44aaf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.8",
      "date": "2026-06-05T08:08:10.000Z",
      "arch": "x86_64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "9e46fa8e4805d3b7a7651717f3c2989dbfe93bc24c4546e7b529939449f4fb24",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.8",
      "date": "2026-06-05T08:06:19.000Z",
      "arch": "emscripten",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "349cf66a483473befa667b1cd685ec5926a0f0298c597ffc28c49ae12c6272fe",
      "status": "success",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.8",
      "date": "2026-06-05T08:05:34.000Z",
      "arch": "x86_64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "c3b7c63ac3a85a5d925e1b96857afc438b24e00aebdf3b67665e2e4830208483",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.8",
      "date": "2026-06-05T08:05:31.000Z",
      "arch": "x86_64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "45a8c42b2b92ef233a88cfd6998b953fc35b2dec6c545a690c0d33598512a36a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.1.8",
      "date": "2026-06-05T08:05:40.000Z",
      "arch": "x86_64",
      "commit": "68b48e6704780019127f358aa2cfbb2424e231ea",
      "fileid": "21087c2fb0cdd622c410f5396996e5f8d1a2875a5923b5897c0aa975d81732c9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/larssnip/actions/runs/27003146725"
    }
  ]
}