{ "_id": "6a1027afacfb0bcc41c90407", "Package": "specL", "Type": "Package", "Title": "specL - Prepare Peptide Spectrum Matches for Use in Targeted\nProteomics", "Version": "1.47.0", "Authors@R": "c(person(\"Christian\", \"Panse\", \nemail = \"cp@fgcz.ethz.ch\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-1975-3064\")),\nperson(\"Jonas\", \"Grossmann\",\nemail = \"jg@fgcz.ethz.ch\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-6899-9020\")),\nperson(\"Christian\", \"Trachsel\",\nrole = \"aut\"),\nperson(\"Witold E.\", \"Wolski\",\nemail = \"wew@fgcz.ethz.ch\",\nrole = \"ctb\"))", "Description": "provides a functions for generating spectra libraries that\ncan be used for MRM SRM MS workflows in proteomics. The package\nprovides a BiblioSpec reader, a function which can add the\nprotein information using a FASTA formatted amino acid file,\nand an export method for using the created library in the\nSpectronaut software. The package is developed, tested and used\nat the Functional Genomics Center Zurich .", "License": "GPL-3", "URL": "http://bioconductor.org/packages/specL/", "Collate": "read.bibliospec.R genSwathIonLib.R annotate.protein_id.R\nAllGenerics.R specL.R specLSet.R cdsw.R zzz.R", "biocViews": "MassSpectrometry, Proteomics", "LazyData": "true", "BugReports": "https://github.com/fgcz/specL/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:12 UTC", "RemoteUrl": "https://github.com/bioc/specL", "RemoteRef": "HEAD", "RemoteSha": "e53853a540e31221948de74931980c6139d5fa7b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 09:50:12 UTC", "User": "root" }, "Author": "Christian Panse [aut, cre] (ORCID:\n),\nJonas Grossmann [aut] (ORCID: ),\nChristian Trachsel [aut],\nWitold E. Wolski [ctb]", "Maintainer": "Christian Panse ", "MD5sum": "8e72b3e0514329ddecb2d38f20e1caf4", "_user": "bioc", "_type": "src", "_file": "specL_1.47.0.tar.gz", "_fileid": "af43b1e8cd95b0452709c0d53fc529af639bd937b253f9ec6541d7430412e015", "_filesize": 1729335, "_sha256": "af43b1e8cd95b0452709c0d53fc529af639bd937b253f9ec6541d7430412e015", "_created": "2026-05-22T09:50:12.000Z", "_published": "2026-05-22T09:53:51.915Z", "_jobs": [ { "job": 77356405545, "time": 127, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7157710178" }, { "job": 77356405557, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7157722608" }, { "job": 77356405580, "time": 185, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7157727284" }, { "job": 77356405595, "time": 122, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7157708693" }, { "job": 77356405581, "time": 124, "config": 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"committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380012 }, "_maintainer": { "name": "Christian Panse", "email": "cp@fgcz.ethz.ch", "login": "cpanse", "mastodon": "@hb9feb@fosstodon.org", "linkedin": "in/cpanse", "orcid": "0000-0003-1975-3064", "description": "proteome informatics; ms comp; visualization; maps; code; reproducible research\n@hb9feb@fosstodon.org", "uuid": 4901987 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "DBI", "version": ">= 0.5", "role": "Depends" }, { "package": "methods", "version": ">= 3.3", "role": "Depends" }, { "package": "protViz", "version": ">= 0.7", "role": "Depends" }, { "package": "RSQLite", "version": ">= 1.1", "role": "Depends" }, { "package": "seqinr", "version": ">= 3.3", "role": "Depends" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "BiocStyle", "version": ">= 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Wolski", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Workflow", "Prologue - How to get the input for the specL package?", "Read from redundant plus non-redundant blib files", "Read from Mascot result files", "Annotate protein IDs using FASTA", "Generate the spectral library (assay)", "Normalizing the retention time using iRT peptides", "Generate the spectral library having no iRTs", "Write output to file", "Epilogue", "What can I do with that library now?", "Benchmark", "Acknowledgement", "TODO for next releases", "Session information", "References" ], "created": "2022-12-07 07:58:07", "modified": "2022-12-08 14:13:07", "commits": 4 } ], "_score": 5.421603926869832, "_indexed": true, "_nocasepkg": "specl", "_universes": [ "bioc", "cpanse", "fgcz" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-05-22T09:52:50.000Z", "distro": "noble", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "5c98c671f544ffa429c4cf04f57b150934bd9461d8e3f5e7e8b666f785d1ba22", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" }, { "r": "4.6.0", "os": "linux", "version": "1.47.0", "date": "2026-05-22T09:53:10.000Z", "distro": "noble", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "7a99b24b37f4c8ee09b242fb97f0ab54ab99e645a17a581a126c6d62299d32e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-05-22T09:52:08.000Z", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "f4cd1f8b27be7b22da95c3a912bd7759ca9e033c0bac25a6c85cb33003a6ed22", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" }, { "r": "4.6.0", "os": "mac", "version": "1.47.0", "date": "2026-05-22T09:52:13.000Z", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "79f5536a55416c65dc70d125eb719122715cd54714f607ed64f6f9a82053200c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-05-22T09:52:16.000Z", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "62474e30df775a3bad3ad7ec56cc97957474840c3bf591b241ed9b384079aecc", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-05-22T09:52:25.000Z", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "89e9e257fe51b4787b0a4b249300cc0d39caa479fa6e0810a9a4c1072d3addf2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-05-22T09:52:07.000Z", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "11ffca57c131bfe3c7e9071f10cb80880b361cb0bc52e4dd72a463b876d54a52", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" }, { "r": "4.6.0", "os": "win", "version": "1.47.0", "date": "2026-05-22T09:51:22.000Z", "commit": "e53853a540e31221948de74931980c6139d5fa7b", "fileid": "767cdfe7efcd8839cb1592cfc666816735d4a7df8efec8f2d828a5652f98f68a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26280696504" } ] }