{ "_id": "6a16a781acfb0bcc41d83305", "Package": "bioseq", "Type": "Package", "Title": "A Toolbox for Manipulating Biological Sequences", "Version": "0.1.5", "Authors@R": "c(person(given = \"Francois\",\nfamily = \"Keck\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"francois.keck@gmail.com\",\ncomment = c(ORCID = \"0000-0002-3323-4167\"))\n)", "Description": "Classes and functions to work with biological sequences\n(DNA, RNA and amino acid sequences). Implements S3\ninfrastructure to work with biological sequences as described\nin Keck (2020) . Provides a\ncollection of functions to perform biological conversion among\nclasses (transcription, translation) and basic operations on\nsequences (detection, selection and replacement based on\npositions or patterns). The package also provides functions to\nimport and export sequences from and to other package formats.", "License": "GPL-3", "URL": "https://fkeck.github.io/bioseq/", "BugReports": "https://github.com/fkeck/bioseq/issues", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "RoxygenNote": "7.2.1", "Config/pak/sysreqs": "libicu-dev libx11-dev", "Repository": "https://fkeck.r-universe.dev", "Date/Publication": "2025-09-29 14:24:15 UTC", "RemoteUrl": "https://github.com/fkeck/bioseq", "RemoteRef": "HEAD", "RemoteSha": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 08:09:02 UTC", "User": "root" }, "Author": "Francois Keck [aut, cre, cph] (ORCID:\n)", "Maintainer": "Francois Keck ", "MD5sum": "6be35e57a76e1d950f8164c7ad850aee", "_user": "fkeck", "_type": "src", "_file": "bioseq_0.1.5.tar.gz", "_fileid": "ab3162f894ce813db5b30a754506887e0614add0e7592e9cc59b7321a2a5ce68", "_filesize": 1106223, "_sha256": "ab3162f894ce813db5b30a754506887e0614add0e7592e9cc59b7321a2a5ce68", "_created": "2026-05-27T08:09:02.000Z", "_published": "2026-05-27T08:12:49.566Z", "_distro": "noble", "_jobs": [ { "job": 78034736278, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7235240359" }, { "job": 78034736276, "time": 126, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7235235039" }, { "job": 78034736294, "time": 181, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7235236906" }, { "job": 78034736255, "time": 128, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7235226282" }, { "job": 78034185333, "time": 206, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7235190729" }, { "job": 78034736234, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7235231928" }, { "job": 78034736240, "time": 101, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7235225958" }, { "job": 78034736357, "time": 93, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7235223299" }, { "job": 78034736279, "time": 92, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7235223146" } ], "_buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/fkeck/bioseq", "_commit": { "id": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "author": "fkeck ", "committer": "fkeck ", "message": "v0.1.5\n", "time": 1759155855 }, "_maintainer": { "name": "Francois Keck", "email": "francois.keck@gmail.com", "login": "fkeck", "bluesky": "@francoiskeck.bsky.social", "orcid": "0000-0002-3323-4167", "description": "", "uuid": 9269625 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "vctrs", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "pillar", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "stringdist", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "fkeck", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-39", "n": 4 }, { "week": "2025-40", "n": 3 } ], "_tags": [ { "name": "v0.1.5", "date": "2025-09-29" } ], "_stars": 26, "_contributors": [ { "user": "fkeck", "count": 121, "uuid": 9269625 }, { "user": "erdaradungaztea", "count": 4, "uuid": 32573962 }, { "user": "hadley", "count": 1, "uuid": 4196 } ], "_userbio": { "uuid": 9269625, "type": "user", "name": "François Keck" }, "_downloads": { "count": 504, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bioseq" }, "_mentions": 1, "_devurl": "https://github.com/fkeck/bioseq", "_pkgdown": "https://fkeck.github.io/bioseq/", "_searchresults": 80, "_rbuild": "4.6.0", "_assets": [ "extra/bioseq.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/fkeck/bioseq", "_realowner": "fkeck", "_cranurl": true, "_releases": [ { "version": "0.1.1", "date": "2020-07-27" }, { "version": "0.1.2", "date": "2020-11-26" }, { "version": "0.1.3", "date": "2021-09-03" }, { "version": "0.1.4", "date": "2022-09-06" }, { "version": "0.1.5", "date": "2025-09-29" } ], "_exports": [ "aa", "aliview", "as_aa", "as_AAbin", "as_dna", "as_DNAbin", "as_rna", "as_seqinr_alignment", "as_tibble.AAbin", "as_tibble.bioseq_aa", "as_tibble.bioseq_dna", "as_tibble.bioseq_rna", "as_tibble.DNAbin", "dna", "is_aa", "is_dna", "is_rna", "new_aa", "new_dna", "new_rna", "pillar_shaft.bioseq_aa", "pillar_shaft.bioseq_dna", "pillar_shaft.bioseq_rna", "read_fasta", "rna", "seaview", "seq_cluster", "seq_combine", "seq_complement", "seq_consensus", "seq_count_pattern", "seq_crop_pattern", "seq_crop_position", "seq_detect_pattern", "seq_disambiguate_IUPAC", "seq_extract_pattern", "seq_extract_position", "seq_nchar", "seq_nseq", "seq_remove_pattern", "seq_remove_position", "seq_replace_pattern", "seq_replace_position", "seq_rev_transcribe", "seq_rev_translate", "seq_reverse", "seq_spellout", "seq_split_kmer", "seq_split_pattern", "seq_stat_gc", "seq_stat_prop", "seq_transcribe", "seq_translate", "validate_seq", "vec_cast.bioseq_aa", "vec_cast.bioseq_dna", "vec_cast.bioseq_rna", "vec_ptype2.bioseq_aa", "vec_ptype2.bioseq_dna", "vec_ptype2.bioseq_rna", "write_fasta" ], "_datasets": [ { "name": "fragilaria", "title": "DNA sequences (rbcL) for various Fragilaria", "object": "fragilaria", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "aa", "title": "Build an amino acid (AA) vector", "concept": [ "classes" ], "topics": [ "aa" ] }, { "page": "aliview", "title": "AliView: DNA sequences viewer", "concept": [ "GUI wrappers" ], "topics": [ "aliview" ] }, { "page": "alphabets", "title": "Biological alphabets", "topics": [ "alphabets" ] }, { "page": "as_aa", "title": "Coercion to an amino acid (AA) vector", "concept": [ "conversions" ], "topics": [ "as_aa" ] }, { "page": "as_AAbin", "title": "Coerce to AAbin", "concept": [ "conversions" ], "topics": [ "as_AAbin" ] }, { "page": "as_AAbin.tbl_df", "title": "Coerce tibble to AAbin", "topics": [ "as_AAbin.tbl_df" ] }, { "page": "as_dna", "title": "Coercion to DNA vector", "concept": [ "conversions" ], "topics": [ "as_dna" ] }, { "page": "as_DNAbin", "title": "Coerce to DNAbin", "concept": [ "conversions" ], "topics": [ "as_DNAbin" ] }, { "page": "as_DNAbin.tbl_df", "title": "Coerce tibble to DNAbin", "topics": [ "as_DNAbin.tbl_df" ] }, { "page": "as_rna", "title": "Coercion to RNA vector", "concept": [ "conversions" ], "topics": [ "as_rna" ] }, { "page": "as_seqinr_alignment", "title": "Coerce to seqinr alignment", "concept": [ "conversions" ], "topics": [ "as_seqinr_alignment" ] }, { "page": "as-tibble-ape", "title": "Convert DNAbin/AAbin to tibble", "concept": [ "conversions" ], "topics": [ "as-tibble-ape", "as_tibble.AAbin", "as_tibble.DNAbin" ] }, { "page": "as-tibble-bioseq", "title": "Convert bioseq DNA, RNA and AA to tibble", "concept": [ "conversions" ], "topics": [ "as-tibble-bioseq", "as_tibble.bioseq_aa", "as_tibble.bioseq_dna", "as_tibble.bioseq_rna" ] }, { "page": "dic_genetic_codes", "title": "Genetic code tables", "topics": [ "dic_genetic_codes" ] }, { "page": "dna", "title": "Build a DNA vector", "concept": [ "classes" ], "topics": [ "dna" ] }, { "page": "fragilaria", "title": "DNA sequences (rbcL) for various Fragilaria", "topics": [ "fragilaria" ] }, { "page": "genetic-codes", "title": "Genetic code tables", "topics": [ "genetic-codes" ] }, { "page": "is_aa", "title": "Test if the object is an amino acid vector", "topics": [ "is_aa" ] }, { "page": "is_dna", "title": "Test if the object is a DNA vector", "topics": [ "is_dna" ] }, { "page": "is_rna", "title": "Test if the object is a RNA vector", "topics": [ "is_rna" ] }, { "page": "new_aa", "title": "Amino acid (AA) vector constructor", "topics": [ "new_aa" ] }, { "page": "new_dna", "title": "DNA vector constructor", "topics": [ "new_dna" ] }, { "page": "new_rna", "title": "RNA vector constructor", "topics": [ "new_rna" ] }, { "page": "read_fasta", "title": "Read sequences in FASTA format", "concept": [ "input/output operations" ], "topics": [ "read_fasta" ] }, { "page": "rev_complement", "title": "Reverse and complement sequences", "concept": [ "biological operations" ], "topics": [ "rev_complement", "seq_complement", "seq_reverse" ] }, { "page": "rna", "title": "Build a RNA vector", "concept": [ "classes" ], "topics": [ "rna" ] }, { "page": "seaview", "title": "SeaView: DNA sequences and phylogenetic tree viewer", "concept": [ "GUI wrappers" ], "topics": [ "seaview" ] }, { "page": "seq_cluster", "title": "Cluster sequences by similarity", "concept": [ "aggregation operations" ], "topics": [ "seq_cluster" ] }, { "page": "seq_combine", "title": "Combine multiple sequences", "concept": [ "string operations" ], "topics": [ "seq_combine" ] }, { "page": "seq_consensus", "title": "Find a consensus sequence for a set of sequences.", "concept": [ "aggregation operations" ], "topics": [ "seq_consensus" ] }, { "page": "seq_count_pattern", "title": "Count the number of matches in sequences", "concept": [ "string operations" ], "topics": [ "seq_count_pattern" ] }, { "page": "seq_crop_pattern", "title": "Crop sequences using delimiting patterns", "concept": [ "string operations" ], "topics": [ "seq_crop_pattern" ] }, { "page": "seq_crop_position", "title": "Crop sequences between two positions", "concept": [ "string operations" ], "topics": [ "seq_crop_position" ] }, { "page": "seq_detect_pattern", "title": "Detect the presence of patterns in sequences", "concept": [ "string operations" ], "topics": [ "seq_detect_pattern" ] }, { "page": "seq_disambiguate_IUPAC", "title": "Disambiguate biological sequences", "concept": [ "op-misc" ], "topics": [ "seq_disambiguate_IUPAC" ] }, { "page": "seq_extract_pattern", "title": "Extract matching patterns from sequences", "concept": [ "string operations" ], "topics": [ "seq_extract_pattern" ] }, { "page": "seq_extract_position", "title": "Extract a region between two positions in sequences", "concept": [ "string operations" ], "topics": [ "seq_extract_position" ] }, { "page": "seq_nchar", "title": "Count the number of character in sequences", "concept": [ "op-misc" ], "topics": [ "seq_nchar" ] }, { "page": "seq_nseq", "title": "Number of sequences in a vector", "concept": [ "op-misc" ], "topics": [ "seq_nseq" ] }, { "page": "seq_remove_pattern", "title": "Remove matched patterns in sequences", "concept": [ "string operations" ], "topics": [ "seq_remove_pattern" ] }, { "page": "seq_remove_position", "title": "Remove a region between two positions in sequences.", "concept": [ "string operations" ], "topics": [ "seq_remove_position" ] }, { "page": "seq_replace_position", "title": "Replace a region between two positions in sequences", "concept": [ "string operations" ], "topics": [ "seq_replace_position" ] }, { "page": "seq_rev_translate", "title": "Reverse translate amino acid sequences", "concept": [ "biological operations" ], "topics": [ "seq_rev_translate" ] }, { "page": "seq_spellout", "title": "Spell out sequences", "concept": [ "op-misc" ], "topics": [ "seq_spellout" ] }, { "page": "seq_split_kmer", "title": "Split sequences into k-mers", "concept": [ "string operations" ], "topics": [ "seq_split_kmer" ] }, { "page": "seq_split_pattern", "title": "Split sequences", "concept": [ "string operations" ], "topics": [ "seq_split_pattern" ] }, { "page": "seq_stat_gc", "title": "Compute G+C content", "concept": [ "op-misc" ], "topics": [ "seq_stat_gc" ] }, { "page": "seq_stat_prop", "title": "Compute proportions for characters", "concept": [ "op-misc" ], "topics": [ "seq_stat_prop" ] }, { "page": "seq_translate", "title": "Translate DNA/RNA sequences into amino acids", "concept": [ "biological operations" ], "topics": [ "seq_translate" ] }, { "page": "seq-replace", "title": "Replace matched patterns in sequences", "concept": [ "string operations" ], "topics": [ "seq-replace", "seq_replace_pattern" ] }, { "page": "transcription", "title": "Transcribe DNA, reverse-transcribe RNA", "concept": [ "biological operations" ], "topics": [ "seq_rev_transcribe", "seq_transcribe", "transcription" ] }, { "page": "write_fasta", "title": "Write sequences in FASTA format", "concept": [ "input/output operations" ], "topics": [ "write_fasta" ] } ], "_pkglogo": "https://github.com/fkeck/bioseq/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/fkeck/bioseq/raw/HEAD/README.md", "_rundeps": [ "ape", "bit", "bit64", "cli", "clipr", "cpp11", "crayon", "digest", "dplyr", "generics", "glue", "hms", "lattice", "lifecycle", "magrittr", "nlme", "pillar", "pkgconfig", "prettyunits", "progress", "R6", "Rcpp", "readr", "rlang", "stringdist", "stringi", "stringr", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr" ], "_vignettes": [ { "source": "ref_database.Rmd", "filename": "ref_database.html", "title": "Cleaning and exploring NCBI data with the bioseq package", "engine": "knitr::rmarkdown", "headings": [ "Loading packages", "Loading data", "Cropping sequences", "Consensus sequences and phylogeny", "Clustering sequences", "Exporting data" ], "created": "2020-05-11 13:19:06", "modified": "2022-08-11 14:55:15", "commits": 8 }, { "source": "intro-bioseq.Rmd", "filename": "intro-bioseq.html", "title": "Introduction to the bioseq package", "engine": "knitr::rmarkdown", "headings": [ "First steps", "Operations on sequences", "Biological conversion among classes", "String operations", "Detection and selection", "Remove and replace" ], "created": "2020-05-11 13:19:06", "modified": "2020-05-11 14:10:07", "commits": 2 } ], "_score": 7.698274576674368, "_indexed": true, "_nocasepkg": "bioseq", "_universes": [ "fkeck" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.5", "date": "2026-05-27T08:11:29.000Z", "distro": "noble", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "a61e8c94e774da8cc7697b17ab3f381a422f027569080443abdf334e3cd59faa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" }, { "r": "4.6.0", "os": "linux", "version": "0.1.5", "date": "2026-05-27T08:11:12.000Z", "distro": "noble", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "b6d58e680e6d8b7f023305e1c682dc35dee7b176770c0e609f091407546f205a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" }, { "r": "4.5.3", "os": "mac", "version": "0.1.5", "date": "2026-05-27T08:11:23.000Z", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "e79748ec8443b8f7bbbb0e6a214a288c4d3f1f07ef01a66db728529a305c246a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" }, { "r": "4.6.0", "os": "mac", "version": "0.1.5", "date": "2026-05-27T08:10:54.000Z", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "14889de84b09361f82c0301b4b9fa3cf659266c33da31483e8094b927de7ea90", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.5", "date": "2026-05-27T08:11:23.000Z", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "be4226424c7e98d87c66d913c081c41b01d5ab3cd5fc3a331eaf40b3afe459f0", "status": "success", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" }, { "r": "4.7.0", "os": "win", "version": "0.1.5", "date": "2026-05-27T08:10:38.000Z", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "e0d2e1564ab6b23dc1208c7edbf6d4c777097e8d767896c013785fe8345c18fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" }, { "r": "4.5.3", "os": "win", "version": "0.1.5", "date": "2026-05-27T08:10:29.000Z", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "40a3a7175b8e4930895859ff9ba5f262fcecf7a5fc4156e6f37dd1bc849e6120", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" }, { "r": "4.6.0", "os": "win", "version": "0.1.5", "date": "2026-05-27T08:10:32.000Z", "commit": "90e138a8e75e51eadc59512b779741cd6bd16d0f", "fileid": "e7530caca583fd32d485ba30784b5987b76d498301eda26e11524ec476516927", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/fkeck/actions/runs/26498966436" } ] }