{ "_id": "6a563073ff0138dec5d6bd46", "Package": "microseq", "Type": "Package", "Title": "Basic Biological Sequence Handling", "Version": "2.2.0", "Date": "2026-07-14", "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 ", "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": "8.0.0", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://larssnip.r-universe.dev", "Date/Publication": "2026-07-14 11:49:28 UTC", "RemoteUrl": "https://github.com/larssnip/microseq", "RemoteRef": "HEAD", "RemoteSha": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-14 12:43:01 UTC", "User": "root" }, "Author": "Lars Snipen [aut, cre],\nKristian Hovde Liland [aut]", "_user": "larssnip", "_type": "src", "_file": "microseq_2.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/1963e1e4d215b5ee7a2917eea9ab05f465ed2037f712d2b4ae6c44cfdbee218b", "_filesize": 238446, "_sha256": "1963e1e4d215b5ee7a2917eea9ab05f465ed2037f712d2b4ae6c44cfdbee218b", "_expires": "2026-10-22T12:49:52.000Z", "_created": "2026-07-14T12:43:01.000Z", "_published": "2026-07-14T12:49:54.789Z", "_jobs": [ { "job": 87087269568, "time": 156, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "8311059539" }, { "job": 87087269486, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8311062297" }, { "job": 87087269466, "time": 162, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8311062093" }, { "job": 87087269540, "time": 164, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8311062141" }, { "job": 87087269535, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8311035641" }, { "job": 87087269462, "time": 354, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "8311146731" }, { "job": 87087269498, "time": 122, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8311043364" }, { "job": 87087269493, "time": 342, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8311139529" }, { "job": 87086297151, "time": 258, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8310985682" }, { "job": 87087269476, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8311049376" }, { "job": 87087269452, "time": 128, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8311046052" }, { "job": 87087269547, "time": 114, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8311039672" }, { "job": 87087269542, "time": 140, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8311051364" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453", "_status": "success", "_upstream": "https://github.com/larssnip/microseq", "_commit": { "id": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "author": "Lars-Gustav Snipen ", "committer": "Lars-Gustav Snipen ", "message": "Added the ctranslate function and correspinding Rcpp code. This function will translate a DNA/RNA sequence into a sequence of codons represented by single letter symbols instead of the triplicates.\n", "time": 1784029768 }, "_maintainer": { "name": "Lars Snipen", "email": "lars.snipen@nmbu.no", "login": "larssnip", "description": "", "uuid": 13868182 }, "_distro": "resolute", "_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": 3, "_updates": [ { "week": "2025-29", "n": 1 }, { "week": "2025-38", "n": 3 }, { "week": "2025-41", "n": 1 }, { "week": "2026-29", "n": 1 } ], "_tags": [], "_stars": 4, "_contributors": [ { "user": "larssnip", "count": 57, "uuid": 13868182 }, { "user": "khliland", "count": 1, "uuid": 9257806 }, { "user": "michaelchirico", "count": 1, "uuid": 7606389 } ], "_userbio": { "uuid": 13868182, "type": "user", "name": "Lars Snipen", "followers": 16 }, "_downloads": { "count": 691, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/microseq" }, "_devurl": "https://github.com/larssnip/microseq", "_searchresults": 132, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_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", "ctranslate", "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": "ctranslate", "title": "Translating codons into a single letter alphabet", "topics": [ "ctranslate" ] }, { "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": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 5.579966418965081, "_indexed": true, "_nocasepkg": "microseq", "_universes": [ "larssnip" ], "_previous": "2.1.8", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.2.0", "date": "2026-07-14T12:45:48.000Z", "distro": "resolute", "arch": "aarch64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/f5ce17030656536c3c3993fb01b0630e7fafb5652a80a4b0a82bc10b5886dbed", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.7.0", "os": "linux", "version": "2.2.0", "date": "2026-07-14T12:45:49.000Z", "distro": "resolute", "arch": "x86_64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/63d6771311beae53800c681c3ff0b14930c686351dbce224dbd3c210e61415d5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.6.1", "os": "linux", "version": "2.2.0", "date": "2026-07-14T12:45:52.000Z", "distro": "resolute", "arch": "aarch64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/17a5b271063a51f8552ee48e4d1035ecfedddcb6f46d7bbb07abb381d35a98c9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.6.1", "os": "linux", "version": "2.2.0", "date": "2026-07-14T12:45:49.000Z", "distro": "resolute", "arch": "x86_64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/f3000e11adc919f65e78d2ff6883e2365e27083b4ba6cd51713bf69576f1f8f3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.5.3", "os": "mac", "version": "2.2.0", "date": "2026-07-14T12:44:46.000Z", "arch": "aarch64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/eb1823d3f816d03244f023ecf38116cc15d97c570431e27281777cdfaa18b257", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.5.3", "os": "mac", "version": "2.2.0", "date": "2026-07-14T12:48:17.000Z", "arch": "x86_64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/02765e13f34270834aaf3f49676156349c08bf52c2df8f33140e61732f56e1be", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.6.1", "os": "mac", "version": "2.2.0", "date": "2026-07-14T12:45:09.000Z", "arch": "aarch64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/71a2118d3546e71d386512f900ac04830ba44088d27782fe6ed69ec6ae165491", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.6.1", "os": "mac", "version": "2.2.0", "date": "2026-07-14T12:47:36.000Z", "arch": "x86_64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/4d4b4143ad49e7e653b726938c09bca4a712fb7c73aa6a1e10671cbc7247ac1d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.6.0", "os": "wasm", "version": "2.2.0", "date": "2026-07-14T12:45:36.000Z", "arch": "emscripten", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/67b0de6d478dd12cd8447f91885d601b9165ab74b2dd9dc643679395d059bf5f", "status": "success", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.7.0", "os": "win", "version": "2.2.0", "date": "2026-07-14T12:44:43.000Z", "arch": "x86_64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/e3364af80d63afda6ff13d9c1d3a9ba741fc20da5ee64874402bd15627dbd618", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.5.3", "os": "win", "version": "2.2.0", "date": "2026-07-14T12:44:26.000Z", "arch": "x86_64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/e81edd4e824d8b237f1c1c45810e86e8626ff77f02ff1125a8f452babba5260b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" }, { "r": "4.6.1", "os": "win", "version": "2.2.0", "date": "2026-07-14T12:44:55.000Z", "arch": "x86_64", "commit": "06f12242fc1d825322a90b93a1d5a0b25e5c91bf", "fileid": "https://r2.ropensci.org/7fb79d896be9a51566efc8672980e00ec50cf234514f258878b5388df896b79d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/larssnip/actions/runs/29333289453" } ] }