{ "_id": "6a2a5efd7b7a29ca6003cc8d", "Package": "les", "Type": "Package", "Title": "Identifying Differential Effects in Tiling Microarray Data", "Version": "1.62.0", "Author": "Julian Gehring, Clemens Kreutz, Jens Timmer", "Maintainer": "Julian Gehring ", "Description": "The 'les' package estimates Loci of Enhanced Significance\n(LES) in tiling microarray data. These are regions of\nregulation such as found in differential transcription,\nCHiP-chip, or DNA modification analysis. The package provides a\nuniversal framework suitable for identifying differential\neffects in tiling microarray data sets, and is independent of\nthe underlying statistics at the level of single probes.", "License": "GPL-3", "LazyLoad": "yes", "biocViews": "Microarray, DifferentialExpression, ChIPchip,\nDNAMethylation, Transcription", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:34:50 UTC", "RemoteUrl": "https://github.com/bioc/les", "RemoteRef": "RELEASE_3_23", "RemoteSha": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-11 07:03:52 UTC", "User": "root" }, "MD5sum": "1bb50830d4cc78728ee527fcce3612ad", "_user": "bioc-release", "_type": "src", "_file": "les_1.62.0.tar.gz", "_fileid": "235e336d9c7265c87c7ffb2cf4382e92b683aaee3df4d200b4fc8643898e2bb2", "_filesize": 541799, "_sha256": "235e336d9c7265c87c7ffb2cf4382e92b683aaee3df4d200b4fc8643898e2bb2", "_created": "2026-06-11T07:03:52.000Z", "_published": "2026-06-11T07:08:45.597Z", "_jobs": [ { "job": 80739593405, "time": 131, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7557107698" }, { "job": 80739593407, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7557119626" }, { "job": 80739593403, "time": 172, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7557119993" }, { "job": 80739593375, "time": 107, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7557145375" }, { "job": 80739593391, "time": 109, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7557141883" }, { "job": 80739132716, "time": 182, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7557067801" }, { "job": 80739593358, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7557099874" }, { "job": 80739593381, "time": 100, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7557098476" }, { "job": 80739593509, "time": 84, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7557093749" }, { "job": 80739593457, "time": 86, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7557094439" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/les", "_commit": { "id": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "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": 1777379690 }, "_maintainer": { "name": "Julian Gehring", "email": "jg-bioc@gmx.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.13.2", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "fdrtool", "role": "Depends" }, { "package": "boot", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "Biobase", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "parallel", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.63.0", "bioc": "3.24" }, { "branch": "release", "version": "1.62.0", "bioc": "3.23" } ], "_topics": [ "microarray", "differentialexpression", "chipchip", "dnamethylation", "transcription" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 426, "source": "https://www.bioconductor.org/packages/stats/bioc/les" }, "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/les.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "chi2", "ci", "epWeight", "estimate", "export", "gaussWeight", "Les", "plot", "rectangWeight", "regions", "show", "summary", "threshold", "triangWeight" ], "_datasets": [ { "name": "exprs", "title": "Spike-in ChIP-chip data set", "object": "spikeInData", "file": "spikeInData.RData", "class": [ "matrix", "array" ], "fields": [ "1", "1", "1", "2", "2", "2" ], "rows": 452, "table": true, "tojson": true }, { "name": "pos", "title": "Spike-in ChIP-chip data set", "object": "spikeInStat", "file": "spikeInStat.RData", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "pval", "title": "Spike-in ChIP-chip data set", "object": "spikeInStat", "file": "spikeInStat.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "reference", "title": "Spike-in ChIP-chip data set", "object": "spikeInData", "file": "spikeInData.RData", "class": [ "data.frame" ], "fields": [ "chr", "start", "end", "length", "fold", "nProbes" ], "rows": 1, "table": true, "tojson": true } ], "_help": [ { "page": "les-package", "title": "Identifying Differential Effects in Tiling Microarray Data", "topics": [ "les-package", "les" ] }, { "page": "chi2", "title": "chi2", "topics": [ "chi2", "chi2,Les-method", "chi2-methods" ] }, { "page": "ci", "title": "ci", "topics": [ "ci", "ci,Les", "ci,Les-method", "ci-methods" ] }, { "page": "estimate", "title": "estimate", "topics": [ "estimate", "estimate,Les-method", "estimate-methods" ] }, { "page": "export", "title": "export", "topics": [ "export", "export,Les", "export,Les-method", "export-methods" ] }, { "page": "Les-class", "title": "Class 'Les'", "topics": [ "Les-class", "show,Les-method", "summary,Les-method", "[,Les-method", "[<-,Les-method" ] }, { "page": "Les", "title": "Les", "topics": [ "Les", "Les,ANY,numeric-method", "Les-methods" ] }, { "page": "plot", "title": "plot method for class Les", "topics": [ "plot", "plot,Les", "plot,Les-method", "plot-methods" ] }, { "page": "regions", "title": "regions", "topics": [ "regions", "regions,Les", "regions,Les-method", "regions-methods" ] }, { "page": "spikeInData", "title": "Spike-in ChIP-chip data set", "topics": [ "exprs", "reference" ] }, { "page": "spikeInStat", "title": "Spike-in ChIP-chip data set", "topics": [ "pos", "pval" ] }, { "page": "threshold", "title": "threshold", "topics": [ "threshold", "threshold,Les", "threshold,Les-method", "threshold-methods" ] }, { "page": "weighting", "title": "Weighting functions", "topics": [ "epWeight", "gaussWeight", "rectangWeight", "triangWeight", "weighting" ] } ], "_rundeps": [ "bitops", "boot", "caTools", "fdrtool", "gplots", "gtools", "KernSmooth", "RColorBrewer" ], "_vignettes": [ { "source": "les.Rnw", "filename": "les.pdf", "title": "Introduction to the les package: Identifying Differential Effects in Tiling Microarray Data with the Loci of Enhanced Significance Framework", "engine": "utils::Sweave", "headings": [ "Introduction", "Data set and statistic testing on probe level", "Incorporation of neighboring probes", "Parameter estimation", "Calculation of confidence intervals", "Visualization", "Exporting results to external software", "Specification of custom weighting windows" ], "created": "2013-07-19 16:22:33", "modified": "2013-07-19 16:22:33", "commits": 1 } ], "_score": 3.778151250383644, "_indexed": false, "_nocasepkg": "les", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/les", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.62.0", "date": "2026-06-11T07:06:38.000Z", "distro": "noble", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "4ce7135c030ccbca63cafcc69735b8f846a92bfcb4e2037a07f4f77a562f5354", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" }, { "r": "4.6.0", "os": "linux", "version": "1.62.0", "date": "2026-06-11T07:06:40.000Z", "distro": "noble", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "fa6562ab948d720d310f5a127b065136d7ff3fc08f4b4102ceac4ff6df6c58ab", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" }, { "r": "4.5.3", "os": "mac", "version": "1.62.0", "date": "2026-06-11T07:08:13.000Z", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "487c5636c52106d38f459dd032855197d7c04b03a5aec266c5ee7250c1264b6e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" }, { "r": "4.6.0", "os": "mac", "version": "1.62.0", "date": "2026-06-11T07:07:54.000Z", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "61f9f0e6e98411beb28a78a6bbd00b1cbbacadf89b3f51be439f5ff94fbe6b9b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" }, { "r": "4.6.0", "os": "wasm", "version": "1.62.0", "date": "2026-06-11T07:05:56.000Z", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "d2646425ee6fa36d8a9ad74954ce658856bdb21b33d30c4dcd3cb42e5315c846", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" }, { "r": "4.7.0", "os": "win", "version": "1.62.0", "date": "2026-06-11T07:05:13.000Z", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "ab109abe3bcbe9077443410d5b8f8e7e4ee741230b29619234f1c53eec466a63", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" }, { "r": "4.5.3", "os": "win", "version": "1.62.0", "date": "2026-06-11T07:04:56.000Z", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "839c1fc1ca1974783cbdec148c8f9a11c1f401741d813d6f411aa332969f6588", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" }, { "r": "4.6.0", "os": "win", "version": "1.62.0", "date": "2026-06-11T07:04:56.000Z", "commit": "d7d9b97a20428bec2dfc86dec573995e0b1f4694", "fileid": "a6e5a81b6263302377f424e1ad0bfbf8f1084810401a0ac7439b96f2cea0d6f9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329764139" } ] }