{ "_id": "6ac640f9f511ae58c09a8d43", "Package": "concatipede", "Title": "Easy Concatenation of Fasta Sequences", "Version": "1.0.1", "Authors@R": "c(\nperson(given = \"Matteo\",\nfamily = \"Vecchi\",\nrole = c(\"aut\", \"cre\"),\nemail = \"matteo.vecchi15@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7995-6827\")),\nperson(given = \"Mattieu\",\nfamily = \"Bruneaux\",\nrole = c(\"aut\"),\nemail = \"matthieu.bruneaux@gmail.com\",\ncomment = c(ORCID = \"0000-0001-6997-192X\")))", "Description": "Concatenation of multiple sequence alignments based on a\ncorrespondence table that can be edited in Excel\n.", "License": "MIT + file LICENSE", "URL": "https://github.com/tardipede/concatipede,\nhttps://tardipede.github.io/concatipede/", "BugReports": "https://github.com/tardipede/concatipede/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr, rmarkdown", "SystemRequirements": "GNU make", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev zlib1g-dev", "Repository": "https://tardipede.r-universe.dev", "Date/Publication": "2022-04-12 07:35:54 UTC", "RemoteUrl": "https://github.com/tardipede/concatipede", "RemoteRef": "HEAD", "RemoteSha": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-07 10:15:44 UTC", "User": "root" }, "Author": "Matteo Vecchi [aut, cre] (ORCID:\n),\nMattieu Bruneaux [aut] (ORCID: )", "Maintainer": "Matteo Vecchi ", "_user": "tardipede", "_type": "src", "_file": "concatipede_1.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/9918f413ae4dbbd4bc1a520873f469f41b0a5b22e4d3f0a9d27f78d8f841f2c7", "_filesize": 2113598, "_sha256": "9918f413ae4dbbd4bc1a520873f469f41b0a5b22e4d3f0a9d27f78d8f841f2c7", "_expires": "2027-01-15T12:54:16.000Z", "_created": "2026-10-07T10:15:44.000Z", "_published": "2026-10-07T12:54:17.783Z", "_buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 112742317084, "time": 145, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11475221822" }, { "job": 112742317233, "time": 131, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11474453776" }, { "job": 112742317121, "time": 210, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11482579417" }, { "job": 112742317250, "time": 209, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11482664742" }, { "job": 112740953521, "time": 217, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11474369532" }, { "job": 112742317141, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11474508520" }, { "job": 112742317151, "time": 81, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11475072221" }, { "job": 112742317258, "time": 91, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11475186796" }, { "job": 112742317487, "time": 83, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11475121965" } ], "_upstream": "https://github.com/tardipede/concatipede", "_commit": { "id": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "author": "Matteo Vecchi <57488469+tardipede@users.noreply.github.com>", "committer": "GitHub ", "message": "Update NAMESPACE\n\nAdded export(rename_sequences)", "time": 1649748954 }, "_maintainer": { "name": "Matteo Vecchi", "email": "matteo.vecchi15@gmail.com", "login": "tardipede", "twitter": "@pittaro90", "description": "", "uuid": 57488469, "orcid": "0000-0002-7995-6827" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "ape", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "qualV", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "readxl", "role": "Imports" }, { "package": "stringdist", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "writexl", "role": "Imports" }, { "package": "DT", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "tardipede", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "tardipede", "count": 140, "uuid": 57488469 }, { "user": "matthieu-bruneaux", "count": 106, "uuid": 5851745 } ], "_userbio": { "uuid": 57488469, "type": "user", "name": "Matteo Vecchi", "followers": 0 }, "_downloads": { "count": 357, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/concatipede" }, "_devurl": "https://github.com/tardipede/concatipede", "_pkgdown": "https://tardipede.github.io/concatipede/", "_searchresults": 7, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/concatipede.html", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/tardipede/concatipede", "_realowner": "tardipede", "_cranurl": true, "_releases": [ { "version": "1.0.1", "date": "2021-08-06" } ], "_exports": [ "%>%", "auto_match_seqs", "concatipede", "concatipede_example", "concatipede_prepare", "find_fasta", "get_genbank_table", "read_xl", "rename_sequences", "write_fasta", "write_nexus", "write_phylip", "write_xl" ], "_help": [ { "page": "auto_match_seqs", "title": "Build a template table with automatically matched sequence names", "topics": [ "auto_match_seqs" ] }, { "page": "concatipede", "title": "Concatenate alignments", "topics": [ "concatipede" ] }, { "page": "concatipede_example", "title": "Get the path to one of concatipede example files", "topics": [ "concatipede_example" ] }, { "page": "concatipede_prepare", "title": "Load alignments and prepare template correspondence table for concatenate () function", "topics": [ "concatipede_prepare" ] }, { "page": "find_fasta", "title": "Find fasta files present in a folder", "topics": [ "find_fasta" ] }, { "page": "get_genbank_table", "title": "Extract GenBank accession number from correspondence table", "topics": [ "get_genbank_table" ] }, { "page": "read_xl", "title": "Read an Excel file", "topics": [ "read_xl" ] }, { "page": "rename_sequences", "title": "Rename sequences", "topics": [ "rename_sequences" ] }, { "page": "write_aln", "title": "Writing alignments", "topics": [ "write_aln", "write_fasta", "write_nexus", "write_phylip" ] }, { "page": "write_xl", "title": "Write an Excel file", "topics": [ "write_xl" ] } ], "_readme": "https://github.com/tardipede/concatipede/raw/HEAD/README.md", "_rundeps": [ "ape", "cellranger", "cli", "cpp11", "crayon", "digest", "dplyr", "generics", "glue", "hms", "igraph", "KernSmooth", "lattice", "lifecycle", "magrittr", "Matrix", "nlme", "pillar", "pkgconfig", "prettyunits", "progress", "qualV", "R6", "Rcpp", "readxl", "rematch", "rlang", "stringdist", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "withr", "writexl" ], "_vignettes": [ { "source": "Package-usage.Rmd", "filename": "Package-usage.html", "title": "Example of package usage", "engine": "knitr::rmarkdown", "headings": [ "Concatipede requirements and workflow", "How to use concatipede", "Prepare the files", "Set up the template for the correspondence table", "Modify the correspondence table", "Concatenate the alignents", "Accessory functions", "get_genbank_table()", "rename_sequences()", "Sequence names automatching" ], "created": "2021-03-11 12:20:10", "modified": "2021-08-05 07:50:05", "commits": 24 } ], "_score": 3.6989700043360187, "_indexed": true, "_nocasepkg": "concatipede", "_universes": [ "tardipede" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-10-07T10:18:06.000Z", "distro": "resolute", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/b055f8a18d2ec870d1b9cd9044d458d45e0b170f8e13eed5199277394aa42fdf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" }, { "r": "4.6.1", "os": "linux", "version": "1.0.1", "date": "2026-10-07T10:17:56.000Z", "distro": "resolute", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/fbe41f0fbb3b6336297f22efa51394c351b1b6dbfe220d01f2c88a1f6ae1089d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-10-07T12:51:32.000Z", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/7eda1881ee50e3aefcd98e9d031c4e8d776dfeb9771369e343571aa1d8d53be2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" }, { "r": "4.6.1", "os": "mac", "version": "1.0.1", "date": "2026-10-07T12:52:46.000Z", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/21ccdef26a913ff136d18f8c65b1320fdbce42e0cc8e5bc693e865b5ac5358c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-10-07T10:18:06.000Z", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/bc49922a55b402b026c433b7f066ff4857cc2b8599893e5037151c690af98aad", "status": "success", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-10-07T10:16:56.000Z", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/e7877e757f3739c679a544912adecf08a394a7e6bc8824ba15058298c8e713fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-10-07T10:17:05.000Z", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/f53929fc721834cf3be46af024aa002a465f986e5d623019ad46fc708267fbb9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" }, { "r": "4.6.1", "os": "win", "version": "1.0.1", "date": "2026-10-07T10:16:56.000Z", "commit": "324e787c8910f3d8f2d7aa7468f3f57fab757bd8", "fileid": "https://r2.ropensci.org/922809fac0c25e811cade2361e1a63edca2d77e55069582f5c92577902985e3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/tardipede/actions/runs/37605790072" } ] }