{ "_id": "6a1fe554b401979e7343c108", "Package": "BREW3R.r", "Type": "Package", "Title": "R package associated to BREW3R", "Version": "1.8.0", "Authors@R": "person(given = \"Lucille\",\nfamily = \"Lopez-Delisle\",\nrole = c(\"aut\", \"cre\"),\nemail = \"lucille.delisle@epfl.ch\",\ncomment = c(ORCID = \"0000-0002-1964-4960\"))", "Description": "This R package provide functions that are used in the\nBREW3R workflow. This mainly contains a function that extend a\ngtf as GRanges using information from another gtf (also as\nGRanges). The process allows to extend gene annotation without\nincreasing the overlap between gene ids.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "biocViews": "GenomeAnnotation", "Config/testthat/edition": "3", "URL": "https://github.com/lldelisle/BREW3R.r", "BugReports": "https://github.com/lldelisle/BREW3R.r/issues/", "VignetteBuilder": "knitr", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:02:52 UTC", "RemoteUrl": "https://github.com/bioc/BREW3R.r", "RemoteRef": "RELEASE_3_23", "RemoteSha": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 08:01:39 UTC", "User": "root" }, "Author": "Lucille Lopez-Delisle [aut, cre] (ORCID:\n)", "Maintainer": "Lucille Lopez-Delisle ", "MD5sum": "db3d6a6cb36b3424009bdc6628475175", "_user": "bioc-release", "_type": "src", "_file": "BREW3R.r_1.8.0.tar.gz", "_fileid": "c2e3d34fd955cca3c8bd14597c83f5e62c9b8519ea3e80feb7dad5128b625818", "_filesize": 1858200, "_sha256": "c2e3d34fd955cca3c8bd14597c83f5e62c9b8519ea3e80feb7dad5128b625818", "_created": "2026-06-03T08:01:39.000Z", "_published": "2026-06-03T08:27:00.020Z", "_distro": "noble", "_jobs": [ { "job": 79248661273, "time": 1477, "config": "bioc-checks", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79248661239, "time": 206, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7378989416" }, { "job": 79248661220, "time": 214, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7378992261" }, { "job": 79248661453, "time": 98, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7378953531" }, { "job": 79248661336, "time": 135, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7378966345" }, { "job": 79247989495, "time": 242, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7378918002" }, { "job": 79248661292, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7378964982" }, { "job": 79248661245, "time": 135, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7378966902" }, { "job": 79248661299, "time": 133, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7378965595" }, { "job": 79248661264, "time": 150, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7378970763" } ], "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/BREW3R.r", "_commit": { "id": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381372 }, "_maintainer": { "name": "Lucille Lopez-Delisle", "email": "lucille.delisle@epfl.ch", "orcid": "0000-0002-1964-4960" }, "_registered": true, "_dependencies": [ { "package": "GenomicRanges", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "genomeannotation" ], "_stars": 0, "_contributors": [ { "user": "jwokaty", "count": 2, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 271, "source": "https://www.bioconductor.org/packages/stats/bioc/BREW3R.r" }, "_devurl": "https://github.com/lldelisle/brew3r.r", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/BREW3R.r.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/lldelisle/brew3r.r", "_realowner": "bioc", "_cranurl": false, "_exports": [ "extend_granges" ], "_help": [ { "page": "add_new_exons", "title": "Add new exons", "topics": [ "add_new_exons" ] }, { "page": "adjust_for_collision", "title": "Adjust for collision", "topics": [ "adjust_for_collision" ] }, { "page": "debug_msg", "title": "Display debug messages if verbose allows it", "topics": [ "debug_msg" ] }, { "page": "extend_granges", "title": "Extend GRanges", "topics": [ "extend_granges" ] }, { "page": "extend_using_overlap", "title": "Overlap exons and extend three prime end", "topics": [ "extend_using_overlap" ] }, { "page": "extract_last_exons", "title": "Extract last exons", "topics": [ "extract_last_exons" ] }, { "page": "filter_new_exons", "title": "Filter new exons for collision", "topics": [ "filter_new_exons" ] }, { "page": "five_prime_pos", "title": "Get five prime position", "topics": [ "five_prime_pos" ] }, { "page": "overlap_different_genes", "title": "Get overlaps from different genes", "topics": [ "overlap_different_genes" ] }, { "page": "progression_msg", "title": "Display progression messages if verbose allows it", "topics": [ "progression_msg" ] }, { "page": "three_prime_pos", "title": "Get three prime position", "topics": [ "three_prime_pos" ] } ], "_readme": "https://github.com/bioc/BREW3R.r/raw/RELEASE_3_23/README.md", "_rundeps": [ "BiocGenerics", "generics", "GenomicRanges", "IRanges", "rlang", "S4Vectors", "Seqinfo" ], "_vignettes": [ { "source": "BREW3R.r.Rmd", "filename": "BREW3R.r.html", "title": "BREW3R.r", "author": "Lucille Lopez-Delisle", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Example", "Load dependencies", "Get gtfs", "Convert gtf files to GRanges", "Save annotations", "Extend the GRanges", "Explore your data", "Recompose the GRanges", "Write new GRanges to gtf", "Session Info" ], "created": "2024-02-21 20:47:18", "modified": "2024-04-03 07:08:40", "commits": 2 } ], "_score": 4, "_indexed": false, "_nocasepkg": "brew3r.r", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/BREW3R.r", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.0", "date": "2026-06-03T08:04:32.000Z", "distro": "noble", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "f0bdb8a4c5dec7ccdf0511a3d6ebd7c43c2f9b4e838730576dac9ec386ffccb6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" }, { "r": "4.6.0", "os": "linux", "version": "1.8.0", "date": "2026-06-03T08:04:41.000Z", "distro": "noble", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "2d7a908ac65479939f6d46ed7e478dc1461ab537d84b7c55001ad8dece12d628", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0", "date": "2026-06-03T08:03:13.000Z", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "f8511a7d5b70849a4131159275b194efb67566bade95394547f64ec98f2f608f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" }, { "r": "4.6.0", "os": "mac", "version": "1.8.0", "date": "2026-06-03T08:03:40.000Z", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "4dcb6ff590cbe5844e7bc039d68cea3d8c42b83eafc1a74db6ed5bf101657f95", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.0", "date": "2026-06-03T08:04:15.000Z", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "55ee41c9c06fec75a3adb28b1af717b47fb282c99465d4dea592d62b7912a3f9", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-06-03T08:03:32.000Z", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "5220e0fc711352b6ed80a3b91fab6f25a587509aed95b9c3d096b2ad1aaa71e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" }, { "r": "4.5.3", "os": "win", "version": "1.8.0", "date": "2026-06-03T08:03:21.000Z", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "7508b332f03aa11e02d2cd62d2a6d484336c98464416afaf7f1ac5b2de877ee4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" }, { "r": "4.6.0", "os": "win", "version": "1.8.0", "date": "2026-06-03T08:03:29.000Z", "commit": "d7844e77bea2f7fc78dd54239934f193e300d0b1", "fileid": "9d007ee14d50c7e725ea49a8e0166307741af40adf8f280771e36d68043dd296", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26871571831" } ] }