{ "_id": "6a193446acfb0bcc41dd1bc6", "Package": "Rbowtie", "Type": "Package", "Title": "R bowtie wrapper", "Version": "1.52.0", "Date": "2023-01-29", "Authors@R": "c(person(\"Florian\", \"Hahne\", role = c(\"aut\")),\nperson(\"Anita\", \"Lerch\", role = c(\"aut\")),\nperson(\"Michael\", \"Stadler\", role = c(\"aut\", \"cre\"),\nemail = \"michael.stadler@fmi.ch\",\ncomment = c(ORCID = \"0000-0002-2269-4934\")))", "Maintainer": "Michael Stadler ", "SystemRequirements": "GNU make", "Description": "This package provides an R wrapper around the popular\nbowtie short read aligner and around SpliceMap, a de novo\nsplice junction discovery and alignment tool. The package is\nused by the QuasR bioconductor package. We recommend to use the\nQuasR package instead of using Rbowtie directly.", "License": "Artistic-2.0 | file LICENSE", "LazyLoad": "yes", "URL": "https://github.com/fmicompbio/Rbowtie", "BugReports": "https://github.com/fmicompbio/Rbowtie/issues", "biocViews": "Sequencing, Alignment", "Archs": "x64", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:37:11 UTC", "RemoteUrl": "https://github.com/bioc/Rbowtie", "RemoteRef": "RELEASE_3_23", "RemoteSha": "890c9d501a207b1696770a56eceb052722175236", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 06:09:15 UTC", "User": "root" }, "Author": "Florian Hahne [aut],\nAnita Lerch [aut],\nMichael Stadler [aut, cre] (ORCID:\n)", "MD5sum": "ed4b768485dfa930320ce60cf5720c27", "_user": "bioc-release", "_type": "src", "_file": "Rbowtie_1.52.0.tar.gz", "_fileid": "929c3831c84e039a3e9da99e843f5a5a5f402d36cc925d0826c50f7688da21ab", "_filesize": 760787, "_sha256": "929c3831c84e039a3e9da99e843f5a5a5f402d36cc925d0826c50f7688da21ab", "_created": "2026-05-29T06:09:15.000Z", "_published": "2026-05-29T06:37:58.451Z", "_jobs": [ { "job": 78447658146, "time": 237, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7284306601" }, { "job": 78447658143, "time": 176, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7284293052" }, { "job": 78447658127, "time": 220, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7284302587" }, { "job": 78447658145, "time": 184, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7284294377" }, { "job": 78447658149, "time": 201, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7284298220" }, { "job": 78447658139, "time": 116, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7284463569" }, { "job": 78447658133, "time": 258, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7284626390" }, { "job": 78447658136, "time": 112, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7284596299" }, { "job": 78447658163, "time": 269, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7284632671" }, { "job": 78447121521, "time": 293, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284253807" }, { "job": 78447658129, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78447658147, "time": 162, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7284289803" }, { "job": 78447658151, "time": 152, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7284287740" }, { "job": 78447658137, "time": 160, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7284289443" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Rbowtie", "_commit": { "id": "890c9d501a207b1696770a56eceb052722175236", "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": 1777379831 }, "_maintainer": { "name": "Michael Stadler", "email": "michael.stadler@fmi.ch", "login": "mbstadler", "orcid": "0000-0002-2269-4934", "description": "", "uuid": 13657342 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "utils", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 8, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.53.0", "bioc": "3.24" }, { "branch": "release", "version": "1.52.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "alignment" ], "_stars": 1, "_contributors": [ { "user": "mbstadler", "count": 113, "uuid": 13657342 }, { "user": "dtenenba", "count": 23, "uuid": 2286826 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "hpages", "count": 3, "uuid": 8810451 }, { "user": "mtmorgan", "count": 2, "uuid": 118552 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "csoneson", "count": 1, "uuid": 5628952 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 834, "source": "https://www.bioconductor.org/packages/stats/bioc/Rbowtie" }, "_mentions": 1, "_devurl": "https://github.com/fmicompbio/rbowtie", "_searchresults": 38, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/Rbowtie.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/fmicompbio/rbowtie", "_realowner": "bioc", "_cranurl": false, "_exports": [ "bowtie", "bowtie_build", "bowtie_build_usage", "bowtie_usage", "bowtie_version", "SpliceMap" ], "_help": [ { "page": "Rbowtie-package", "title": "R bowtie wrapper", "topics": [ "Rbowtie-package", "Rbowtie" ] }, { "page": "Rbowtie", "title": "Interface to bowtie", "topics": [ "bowtie", "bowtie_build", "bowtie_build_usage", "bowtie_usage", "bowtie_version" ] }, { "page": "SpliceMap", "title": "Interface to SpliceMap", "topics": [ "SpliceMap" ] } ], "_readme": "https://github.com/bioc/Rbowtie/raw/RELEASE_3_23/README.md", "_rundeps": [], "_vignettes": [ { "source": "Rbowtie-Overview.Rmd", "filename": "Rbowtie-Overview.html", "title": "An introduction to Rbowtie", "author": "Michael Stadler, Dimos Gaidatzis, Anita Lerch", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Preliminaries", "Citing Rbowtie", "Installation", "Loading of Rbowtie", "How to get help", "Example usage for individual Rbowtie functions", "Build the reference index with bowtie_build", "Create alignment with bowtie", "Create spliced alignment with SpliceMap", "Session information", "References" ], "created": "2018-01-06 14:42:44", "modified": "2018-07-19 09:28:50", "commits": 4 } ], "_score": 6.863084825320359, "_indexed": false, "_nocasepkg": "rbowtie", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/Rbowtie", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.52.0", "date": "2026-05-29T06:12:25.000Z", "distro": "noble", "arch": "aarch64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "6459088aa87e98094b69feb8ec31538c8c7a3e24a0700b0f737d00c34774f1ff", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.7.0", "os": "linux", "version": "1.52.0", "date": "2026-05-29T06:13:10.000Z", "distro": "noble", "arch": "x86_64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "3d39a7d74e6761275469ff2262b8998442998c48d6f6ff9530fa788f9c106e8e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.6.0", "os": "linux", "version": "1.52.0", "date": "2026-05-29T06:12:20.000Z", "distro": "noble", "arch": "aarch64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "ab3c758c15cf2518e19ba41ba0a66db6097ce605f573d2e5ff7c3f75a812883f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.6.0", "os": "linux", "version": "1.52.0", "date": "2026-05-29T06:12:36.000Z", "distro": "noble", "arch": "x86_64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "1f8a7c2da0adb91d1bb55200eb4d60322c78c7d51228af8af8f153a31242571f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.5.3", "os": "mac", "version": "1.52.0", "date": "2026-05-29T06:25:08.000Z", "arch": "aarch64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "76bde31920122c36b48f970954dbe28ed57d43d08036a96e5b5d9515bbc9bf1e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.5.3", "os": "mac", "version": "1.52.0", "date": "2026-05-29T06:35:39.000Z", "arch": "x86_64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "e02acc0439a155b0b66b8a5f0aeb7b586fad6ec565a05ccd11ec2c14ed9206d2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.6.0", "os": "mac", "version": "1.52.0", "date": "2026-05-29T06:34:28.000Z", "arch": "aarch64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "c43c0005c3404143c77d8deb8c95d39741e035045b2d207c67e6242228f7c52d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.6.0", "os": "mac", "version": "1.52.0", "date": "2026-05-29T06:35:56.000Z", "arch": "x86_64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "c8c7588ab120e31789bb73687e1041551ca0635f0f1d652e45f64bce66e20f27", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.7.0", "os": "win", "version": "1.52.0", "date": "2026-05-29T06:11:29.000Z", "arch": "x86_64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "c3ef1bcfd20e1512e9398145e8181e14cc70d8b08cc2841c6864eb120f0a6aad", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.5.3", "os": "win", "version": "1.52.0", "date": "2026-05-29T06:11:16.000Z", "arch": "x86_64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "fa6dec9dc7fc1c4df4e20bcffc885b3e308f03c0e7c38da06a353790bb9c8a26", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" }, { "r": "4.6.0", "os": "win", "version": "1.52.0", "date": "2026-05-29T06:11:21.000Z", "arch": "x86_64", "commit": "890c9d501a207b1696770a56eceb052722175236", "fileid": "701f375eef52e917b37802407a3e8dcd10ec4ca2e963885a965874a9c642189f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621132955" } ] }