{ "_id": "6a4990206d67900babdfbab9", "Package": "tRNA", "Title": "Analyzing tRNA sequences and structures", "Version": "1.31.0", "Date": "2025-07-28", "Authors@R": "person(\"Felix GM\", \n\"Ernst\",\nemail = \"felix.gm.ernst@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5064-0928\"))", "Description": "The tRNA package allows tRNA sequences and structures to\nbe accessed and used for subsetting. In addition, it provides\nvisualization tools to compare feature parameters of multiple\ntRNA sets and correlate them to additional data. The tRNA\npackage uses GRanges objects as inputs requiring only few\nadditional column data sets.", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "Software, Visualization", "Collate": "'tRNA.R' 'AllGenerics.R' 'tRNA-checks.R' 'tRNA-dotbracket.R'\n'tRNA-features.R' 'tRNA-plot.R' 'tRNA-sequences.R'\n'tRNA-structures.R' 'tRNA-subset.R' 'tRNA-utils.R' 'utils.R'", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "BugReports": "https://github.com/FelixErnst/tRNA/issues", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:58 UTC", "RemoteUrl": "https://github.com/bioc/tRNA", "RemoteRef": "HEAD", "RemoteSha": "7d43907b846d9aea841a1502086fbca999fcbef2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 22:47:46 UTC", "User": "root" }, "Author": "Felix GM Ernst [aut, cre] (ORCID:\n)", "Maintainer": "Felix GM Ernst ", "_user": "bioc", "_type": "src", "_file": "tRNA_1.31.0.tar.gz", "_fileid": "https://r2.ropensci.org/0a7a8ee0685a95102090a1093a32ddd238da7c8724b36db5d51a5b53c680131a", "_filesize": 1059248, "_sha256": "0a7a8ee0685a95102090a1093a32ddd238da7c8724b36db5d51a5b53c680131a", "_expires": "2026-10-12T22:58:38.000Z", "_created": "2026-07-04T22:47:46.000Z", "_published": "2026-07-04T22:58:40.332Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288", "_status": "success", "_upstream": "https://github.com/bioc/tRNA", "_commit": { "id": "7d43907b846d9aea841a1502086fbca999fcbef2", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380538 }, "_maintainer": { "name": "Felix GM Ernst", "email": "felix.gm.ernst@outlook.com", "login": "felixernst", "description": "", "uuid": 17824332, "orcid": "0000-0001-5064-0928" }, "_distro": "resolute", "_jobs": [ { "job": 85173375798, "time": 189, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8086139334" }, { "job": 85173375814, "time": 339, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8086155800" }, { "job": 85173375806, "time": 307, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8086152253" }, { "job": 85173375811, "time": 221, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8086183589" }, { "job": 85173375810, "time": 163, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8086138324" }, { "job": 85173038467, "time": 341, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8086117999" }, { "job": 85173375823, "time": 147, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8086134722" }, { "job": 85173375821, "time": 229, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8086143849" }, { "job": 85173375816, "time": 226, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8086143814" }, { "job": 85173375820, "time": 241, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8086145173" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "Structstrings", "role": "Depends" }, { "package": "stringr", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "XVector", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "Modstrings", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "tRNAscanImport", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-39", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "software", "visualization", "bioconductor", "sequences", "structures", "trna" ], "_stars": 1, "_contributors": [ { "user": "felixernst", "count": 76, "uuid": 17824332 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 9, "_devurl": "https://github.com/felixernst/trna", "_searchresults": 8, "_rbuild": "4.6.1", "_assets": [ "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", "extra/tRNA.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/felixernst/trna", "_realowner": "bioc", "_cranurl": false, "_exports": [ "gettRNABasePairing", "gettRNAFeaturePlots", "gettRNALoopIDs", "gettRNAstructureGRanges", "gettRNAstructureSeqs", "gettRNASummary", "hasAcceptorStem", "hasAnticodonLoop", "hasAnticodonStem", "hasDloop", "hasDStem", "hasTloop", "hasTStem", "hasVariableLoop", "istRNAGRanges" ], "_datasets": [ { "name": "gr", "title": "tRNA example data", "object": "gr", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "gr_eco", "title": "tRNA example data", "object": "gr_eco", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "gr_human", "title": "tRNA example data", "object": "gr_human", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "gr_human2", "title": "tRNA example data", "object": "gr_human2", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "gettRNABasePairing", "title": "Accessing Dot Bracket annotation of tRNAs", "topics": [ "gettRNABasePairing", "gettRNABasePairing,GRanges-method", "gettRNALoopIDs", "gettRNALoopIDs,GRanges-method" ] }, { "page": "gettRNAFeaturePlots", "title": "Graphical summary of tRNA features", "topics": [ "gettRNAFeaturePlots", "gettRNAFeaturePlots,GRangesList-method" ] }, { "page": "gettRNAstructureSeqs", "title": "tRNA structures and sequences", "topics": [ "gettRNAstructureGRanges", "gettRNAstructureGRanges,GRanges-method", "gettRNAstructureSeqs", "gettRNAstructureSeqs,GRanges-method" ] }, { "page": "gettRNASummary", "title": "Summary of tRNA features", "topics": [ "gettRNASummary", "gettRNASummary,GRanges-method", "gettRNASummary,GRangesList-method" ] }, { "page": "tRNA-subset", "title": "Subsetting tRNAs", "topics": [ "hasAcceptorStem", "hasAcceptorStem,GRanges-method", "hasAnticodonLoop", "hasAnticodonLoop,GRanges-method", "hasAnticodonStem", "hasAnticodonStem,GRanges-method", "hasDloop", "hasDloop,GRanges-method", "hasDStem", "hasDStem,GRanges-method", "hasTloop", "hasTloop,GRanges-method", "hasTStem", "hasTStem,GRanges-method", "hasVariableLoop", "hasVariableLoop,GRanges-method", "tRNA-subset" ] }, { "page": "istRNAGRanges", "title": "tRNA compatibility check", "topics": [ "istRNAGRanges", "istRNAGRanges,GRanges-method" ] }, { "page": "tRNA", "title": "tRNA: analyzing tRNA sequences and structures", "topics": [ "tRNA-package", "tRNA" ] }, { "page": "tRNA-data", "title": "tRNA example data", "topics": [ "gr", "gr_eco", "gr_human", "gr_human2", "tRNA-data" ] } ], "_readme": "https://github.com/bioc/tRNA/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "Biostrings", "cli", "cpp11", "crayon", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lifecycle", "magrittr", "Modstrings", "R6", "RColorBrewer", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "stringi", "stringr", "Structstrings", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "tRNA.Rmd", "filename": "tRNA.html", "title": "Analyzing tRNA sequences and structures", "author": "Felix G.M. Ernst", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Loading tRNA information", "tRNA sequences and structures", "Subsetting tRNA sequences", "Visualization", "Options", "Dot bracket annotation", "Session info" ], "created": "2018-09-07 14:12:10", "modified": "2020-01-21 18:08:32", "commits": 13 } ], "_score": 6.686636269262293, "_indexed": true, "_nocasepkg": "trna", "_universes": [ "bioc", "felixernst" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-07-04T22:51:37.000Z", "distro": "resolute", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/d9b8c6c81d2f29874a5b1bf8d9c387440d620898c44dc91d57089b9c2923d500", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-07-04T22:51:02.000Z", "distro": "resolute", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/38435d6a54b126d6da38d56bbf9e4273617c770c53f0984ed46030b0ca0bf5f0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-07-04T22:56:26.000Z", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/f9120deef0386de363ef4c7d2e6dc4f04f9182cd87d0206226226d96918f7c31", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-07-04T22:49:51.000Z", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/68b59dbb69294384f89581f08621359aebab0a10a8ecf4c1ec60d1ca58f86786", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-07-04T22:50:41.000Z", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/d59f6ed39de83248a1f5944e30baf24bd0f10c0020c5359cdf4dd25c48cdf359", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-07-04T22:49:26.000Z", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/bdf225ef9d0f9bef5f9b998911e7a66641eb5aff51f98f47715ab8e583c7af40", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-07-04T22:49:40.000Z", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/13aceaffc4f8eeb0f409167c7e99f18e1220c03a9374aa826024fdb167308057", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" }, { "r": "4.6.1", "os": "win", "version": "1.31.0", "date": "2026-07-04T22:49:37.000Z", "commit": "7d43907b846d9aea841a1502086fbca999fcbef2", "fileid": "https://r2.ropensci.org/2de69be45ff7a157a9a1435bf3b4beb73bf1acafe53ccf87f71d180d83982fc6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28722005288" } ] }