{ "_id": "6ae5e9488d250e7ad09f4262", "Package": "Rbowtie", "Type": "Package", "Title": "R bowtie wrapper", "Version": "1.53.1", "Date": "2026-07-29", "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\")))", "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.r-universe.dev", "Date/Publication": "2026-07-29 14:49:03 UTC", "RemoteUrl": "https://github.com/bioc/Rbowtie", "RemoteRef": "HEAD", "RemoteSha": "7ca814fdd080e87c2914719eabf777c7454b725f", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-31 11:51:21 UTC", "User": "root" }, "Author": "Florian Hahne [aut],\nAnita Lerch [aut],\nMichael Stadler [aut, cre] (ORCID:\n)", "Maintainer": "Michael Stadler ", "_user": "bioc", "_type": "src", "_file": "Rbowtie_1.53.1.tar.gz", "_fileid": "https://r2.ropensci.org/853d5fb974f309dc468e323b1397b11c34814595698c1b4ea8c2693e36e66299", "_filesize": 760471, "_sha256": "853d5fb974f309dc468e323b1397b11c34814595698c1b4ea8c2693e36e66299", "_expires": "2027-02-08T13:12:38.000Z", "_created": "2026-10-31T11:51:21.000Z", "_published": "2026-10-31T13:12:40.641Z", "_upstream": "https://github.com/bioc/Rbowtie", "_status": "success", "_maintainer": { "name": "Michael Stadler", "email": "michael.stadler@fmi.ch", "login": "mbstadler", "orcid": "0000-0002-2269-4934", "description": "", "uuid": 13657342 }, "_jobs": [ { "job": 124529893002, "time": 198, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "13041996177" }, { "job": 124529893036, "time": 165, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "13041139336" }, { "job": 124529893070, "time": 205, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13041737181" }, { "job": 124529893092, "time": 156, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "13041896579" }, { "job": 124529893084, "time": 274, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "13041493045" }, { "job": 124529893001, "time": 133, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "13044126670" }, { "job": 124529893015, "time": 256, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13041772243" }, { "job": 124529893024, "time": 161, "config": "macos-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13044150975" }, { "job": 124529893004, "time": 344, "config": "macos-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13041538118" }, { "job": 124528821583, "time": 323, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "13040579794" }, { "job": 124529893008, "time": 94, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 124529893111, "time": 252, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "13041194359" }, { "job": 124529893073, "time": 146, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13041806956" }, { "job": 124529893093, "time": 156, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13042185581" }, { "job": 124529893086, "time": 292, "config": "windows-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13042135949" }, { "job": 124529893110, "time": 152, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13041064485" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828", "_commit": { "id": "7ca814fdd080e87c2914719eabf777c7454b725f", "author": "mbstadler ", "committer": "mbstadler ", "message": "update GHA to not use depreciated versions\n\nCo-authored-by: Charlotte Soneson \nCo-authored-by: Michael Stadler \n", "time": 1785336543 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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": true, "_usedby": 8, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-31", "n": 7 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.53.1", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.52.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "sequencing", "alignment" ], "_stars": 1, "_contributors": [ { "user": "mbstadler", "count": 120, "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": "jeroen", "count": 1, "uuid": 216319 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 481, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 966, "source": "https://www.bioconductor.org/packages/stats/bioc/Rbowtie" }, "_mentions": 1, "_devurl": "https://github.com/fmicompbio/rbowtie", "_searchresults": 36, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/Rbowtie.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_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/HEAD/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": 7.0668475109739, "_indexed": true, "_nocasepkg": "rbowtie", "_universes": [ "bioc", "mbstadler", "fmicompbio" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.53.1", "date": "2026-10-31T11:54:26.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/e57fbd05978cc480c5bb7214f66a6d250d0577ae805e37af774908c105454f6a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.7.0", "os": "linux", "version": "1.53.1", "date": "2026-10-31T11:55:10.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/d1a20b3ad241bbc4b7e087218f7cc83808288b22ef1b8136f14086f52d45f643", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.6.1", "os": "linux", "version": "1.53.1", "date": "2026-10-31T11:54:10.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/cfbc71cbd44f0b78f826321c39da69ff8eb4ba1bcc7daf6f0d2ebe9040fdd949", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.6.1", "os": "linux", "version": "1.53.1", "date": "2026-10-31T11:55:50.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/048770c68de97e14d1ced85f11444e072497a20b735620dd35b3675051723f00", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.5.3", "os": "mac", "version": "1.53.1", "date": "2026-10-31T13:10:54.000Z", "arch": "aarch64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/2a4e58b3acfdcb9b508c2a3c1c620a1e69a92462760e5241b5a3b5859cb23266", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.5.3", "os": "mac", "version": "1.53.1", "date": "2026-10-31T11:55:00.000Z", "arch": "x86_64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/de13662d18f42b1700306b0ba574caa859739a0fbf20f8838333e21d78baf89b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.6.2", "os": "mac", "version": "1.53.1", "date": "2026-10-31T13:11:19.000Z", "arch": "aarch64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/21f63dbe18cdc1f95887f9483ca47bf73719da354f9bc086d20ae346964212c3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.6.2", "os": "mac", "version": "1.53.1", "date": "2026-10-31T11:56:26.000Z", "arch": "x86_64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/4e1ef69542e0d57cd767480f66daabc08d2836e3cae303d096ac0c38dcacc052", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.7.0", "os": "win", "version": "1.53.1", "date": "2026-10-31T11:55:02.000Z", "arch": "aarch64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/3f0a4527a326d065527d1237b22d0c6696b1c20c5d1722dd50902e58ff5ae1ea", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.7.0", "os": "win", "version": "1.53.1", "date": "2026-10-31T11:53:18.000Z", "arch": "x86_64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/fab54599b3ca74de79f407302f34085e6f805b622969197b004bd909176f62ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.5.3", "os": "win", "version": "1.53.1", "date": "2026-10-31T11:53:27.000Z", "arch": "x86_64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/bd5ca07da70c6680ef98dc9480fca1487fb177a4d690ee1841654d27815e5976", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.6.2", "os": "win", "version": "1.53.1", "date": "2026-10-31T11:55:45.000Z", "arch": "aarch64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/e91753a8968c9e89864816d88751a17b1a6f2867c0750752551971d420fd5896", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" }, { "r": "4.6.2", "os": "win", "version": "1.53.1", "date": "2026-10-31T11:53:25.000Z", "arch": "x86_64", "commit": "7ca814fdd080e87c2914719eabf777c7454b725f", "fileid": "https://r2.ropensci.org/c0a1bac0983a9b273c7fd30e63ed7fe048e9ef6b1b23964d3bc0ed8860178012", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41198272828" } ] }