{ "_id": "6a548643ff0138dec5d64b5c", "Package": "tAI", "Type": "Package", "Title": "The tRNA Adaptation Index", "Version": "0.2.2", "Date": "2025-03-19", "Authors@R": "person(given = c(\"Mario\"),\nfamily = \"dos Reis\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mariodosreis@gmail.com\")", "Description": "Functions and example files to calculate the tRNA\nadaptation index, a measure of the level of co-adaptation\nbetween the set of tRNA genes and the codon usage bias of\nprotein-coding genes in a given genome. The methodology is\ndescribed in dos Reis, Wernisch and Savva (2003)\n, and dos Reis, Savva and Wernisch\n(2004) .", "License": "GPL (>= 2)", "LazyData": "TRUE", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Repository": "https://mariodosreis.r-universe.dev", "Date/Publication": "2025-04-25 11:36:11 UTC", "RemoteUrl": "https://github.com/mariodosreis/tai", "RemoteRef": "HEAD", "RemoteSha": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-13 06:28:02 UTC", "User": "root" }, "Author": "Mario dos Reis [aut, cre]", "Maintainer": "Mario dos Reis ", "_user": "mariodosreis", "_type": "src", "_file": "tAI_0.2.2.tar.gz", "_fileid": "https://r2.ropensci.org/4ef692bbacd906a8b5c09fcd06c681a60a05f19861e1f589cae763e01d7208e2", "_filesize": 176538, "_sha256": "4ef692bbacd906a8b5c09fcd06c681a60a05f19861e1f589cae763e01d7208e2", "_expires": "2026-10-21T06:31:30.000Z", "_created": "2026-07-13T06:28:02.000Z", "_published": "2026-07-13T06:31:31.851Z", "_jobs": [ { "job": 86749241715, "time": 106, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8270856612" }, { "job": 86749241729, "time": 101, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8270855314" }, { "job": 86749241713, "time": 174, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8270867535" }, { "job": 86749241692, "time": 138, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8270859408" }, { "job": 86748757911, "time": 198, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8270825757" }, { "job": 86749241706, "time": 95, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8270853355" }, { "job": 86749241765, "time": 52, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8270841390" }, { "job": 86749241710, "time": 61, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8270843598" }, { "job": 86749241745, "time": 56, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8270842375" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532", "_status": "success", "_upstream": "https://github.com/mariodosreis/tai", "_commit": { "id": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "author": "Mario dos Reis ", "committer": "Mario dos Reis ", "message": "Update README.md to fix description of MET codon removal (the genomic\ntRNA database does provide seperate counts for iMET and MET tRNA genes)\n", "time": 1745580971 }, "_maintainer": { "name": "Mario dos Reis", "email": "mariodosreis@gmail.com", "login": "mariodosreis", "description": "Evolutionary biologist", "uuid": 11352083 }, "_distro": "resolute", "_registered": true, "_dependencies": [], "_owner": "mariodosreis", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 21, "_contributors": [ { "user": "mariodosreis", "count": 64, "uuid": 11352083 } ], "_userbio": { "uuid": 11352083, "type": "user", "name": "Mario dos Reis", "followers": 39, "description": "Evolutionary biologist" }, "_downloads": { "count": 379, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tAI" }, "_devurl": "https://github.com/mariodosreis/tai", "_searchresults": 16, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/tAI.html", "manual.pdf" ], "_homeurl": "https://github.com/mariodosreis/tai", "_realowner": "mariodosreis", "_cranurl": true, "_releases": [ { "version": "0.2.2", "date": "2025-04-16" } ], "_exports": [ "get.s", "get.tai", "get.ws", "nc.adj", "nc.f", "ts.test" ], "_datasets": [ { "name": "ecolik12", "title": "E. coli K-12 codon bias and tRNA numbers", "object": "ecolik12", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "ecolik12", "title": "E. coli K-12 codon bias and tRNA numbers", "topics": [ "ecolik12" ] }, { "page": "get.s", "title": "Correlation between tAI and Nc adjusted", "topics": [ "get.s" ] }, { "page": "get.tai", "title": "The tRNA adaptation index", "topics": [ "get.tai" ] }, { "page": "get.ws", "title": "Relative adaptiveness values", "topics": [ "get.ws" ] }, { "page": "nc.adj", "title": "Adjusted effective number of codons (Nc)", "topics": [ "nc.adj" ] }, { "page": "nc.f", "title": "Nc vs. GC3s", "topics": [ "nc.f" ] }, { "page": "ts.test", "title": "Monte Carlo test of correlation between tAI and Nc adjusted", "topics": [ "ts.test" ] } ], "_readme": "https://github.com/mariodosreis/tai/raw/HEAD/README.md", "_rundeps": [], "_score": 4.225309281725863, "_indexed": true, "_nocasepkg": "tai", "_universes": [ "mariodosreis" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.2", "date": "2026-07-13T06:29:56.000Z", "distro": "resolute", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/1c42e3d1c1a9c64db795f79f71446a458ab64c2280355eea60dcb1abfb72792e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" }, { "r": "4.6.1", "os": "linux", "version": "0.2.2", "date": "2026-07-13T06:29:51.000Z", "distro": "resolute", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/8b2e68e17335880e626dae049fb85aee6d9af1241c6e4eca7441387c409221fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" }, { "r": "4.5.3", "os": "mac", "version": "0.2.2", "date": "2026-07-13T06:30:32.000Z", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/403b2be52d15bb3f16fc6796cb9b8cd0f75861a22906e2f224ac780baf224936", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" }, { "r": "4.6.1", "os": "mac", "version": "0.2.2", "date": "2026-07-13T06:30:05.000Z", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/55af2b85860031a065375659420b5c948a409a937a9c6d8c100044b580405a3d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.2", "date": "2026-07-13T06:29:52.000Z", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/f9e97bf27a34281f675eb2ba0c37380fefed35fd34bc6ecdd17484ff7a47f461", "status": "success", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" }, { "r": "4.7.0", "os": "win", "version": "0.2.2", "date": "2026-07-13T06:28:59.000Z", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/7afa8b2597e00f2d5fcb9c27c0241b2dff18fb6a6a540584d7a2aeaac6df5a80", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" }, { "r": "4.5.3", "os": "win", "version": "0.2.2", "date": "2026-07-13T06:29:07.000Z", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/4c3e7d4dc7ee1371d0f28335703eba8b1249a4a08ed1cf4f5eda0c0f15b3c1f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" }, { "r": "4.6.1", "os": "win", "version": "0.2.2", "date": "2026-07-13T06:29:02.000Z", "commit": "3a2057dfb000fdc680cfaac0f59417c46b1f20d4", "fileid": "https://r2.ropensci.org/d84ef878d11512d7bd36ff91611bcdcd6da55460f4b7abe5180c4659bd95410c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mariodosreis/actions/runs/29228919532" } ] }