{ "_id": "6ae74f9c1e2c7b3a4f53003d", "Package": "les", "Type": "Package", "Title": "Identifying Differential Effects in Tiling Microarray Data", "Version": "1.63.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:34:50 UTC", "RemoteUrl": "https://github.com/bioc/les", "RemoteRef": "HEAD", "RemoteSha": "6a07807bd6d408a55473c5dd66ce496b985176c0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 13:17:00 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "les_1.63.0.tar.gz", "_fileid": "https://r2.ropensci.org/13573d541e1b73ba8d090dba8cef44e42a004ddd1f88e4664f76d770b5ce34b2", "_filesize": 544250, "_sha256": "13573d541e1b73ba8d090dba8cef44e42a004ddd1f88e4664f76d770b5ce34b2", "_expires": "2027-02-09T14:41:30.000Z", "_created": "2026-11-01T13:17:00.000Z", "_published": "2026-11-01T14:41:32.163Z", "_upstream": "https://github.com/bioc/les", "_status": "success", "_maintainer": { "name": "Julian Gehring", "email": "jg-bioc@gmx.com" }, "_jobs": [ { "job": 124859756347, "time": 115, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13085487049" }, { "job": 124859756370, "time": 157, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13086230651" }, { "job": 124859756369, "time": 189, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13085891953" }, { "job": 124859756500, "time": 111, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13086949957" }, { "job": 124859756437, "time": 104, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13087841514" }, { "job": 124857463316, "time": 163, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13085212106" }, { "job": 124859756337, "time": 80, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13086300876" }, { "job": 124859756421, "time": 94, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13085351858" }, { "job": 124859756381, "time": 101, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13085416378" }, { "job": 124859756394, "time": 85, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13084808963" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150", "_commit": { "id": "6a07807bd6d408a55473c5dd66ce496b985176c0", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379690 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.63.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.62.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microarray", "differentialexpression", "chipchip", "dnamethylation", "transcription" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 584, "source": "https://www.bioconductor.org/packages/stats/bioc/les" }, "_searchresults": 5, "_abi": { "exports": [ { "key": "les::Les", "hash": "201cba6502d9c7d4" }, { "key": "les::generic:Les", "hash": "1211ed226e2da6b2" }, { "key": "les::generic:chi2", "hash": "9da9a37d43ff89c5" }, { "key": "les::generic:ci", "hash": "aff004e942284233" }, { "key": "les::generic:estimate", "hash": "ff46c053b9063a5e" }, { "key": "les::generic:export", "hash": "ee9a428a72a433e0" }, { "key": "les::generic:regions", "hash": "af19cf2526d3a865" }, { "key": "les::generic:threshold", "hash": "350ee6937ee405ab" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/les.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "LICENSE" ], "_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": true, "_nocasepkg": "les", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.63.0", "date": "2026-11-01T13:39:29.000Z", "distro": "resolute", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/554e7ca2536bb99b99bdc437bd553e99de6dd7f2a48b3b45ee40191ab76c4073", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" }, { "r": "4.6.2", "os": "linux", "version": "1.63.0", "date": "2026-11-01T13:40:04.000Z", "distro": "resolute", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/208f2d51fe2bbfd1b3d4ab3ee02dd12ccbed96ef5b2be4195114b036e28c2531", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" }, { "r": "4.5.3", "os": "mac", "version": "1.63.0", "date": "2026-11-01T14:35:07.000Z", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/fb33da25304505795b6b4e406d33a65e1b86ba1b417412c5a9e984ae06a62ac8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" }, { "r": "4.6.2", "os": "mac", "version": "1.63.0", "date": "2026-11-01T14:35:00.000Z", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/63728da2e228bdf0f57c4ec8c0044abe1164d36d8e8da1b4fbd81cd41cc4a52b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" }, { "r": "4.6.0", "os": "wasm", "version": "1.63.0", "date": "2026-11-01T13:38:38.000Z", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/dab2d8ea570e6142493fbb32a72e618fc30e1b0a38a90449d5a1bf9079d13880", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" }, { "r": "4.7.0", "os": "win", "version": "1.63.0", "date": "2026-11-01T13:19:32.000Z", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/dd021b6b1c9423207356642120ed362e3ce9b2c69a488f6df0592ee82ce18da9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" }, { "r": "4.5.3", "os": "win", "version": "1.63.0", "date": "2026-11-01T13:19:46.000Z", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/55bb7021e01b4d59cb98ef95b1bd6a5ffc735f8c351c1a2ac21d3071fa5fb7eb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" }, { "r": "4.6.2", "os": "win", "version": "1.63.0", "date": "2026-11-01T13:19:37.000Z", "commit": "6a07807bd6d408a55473c5dd66ce496b985176c0", "fileid": "https://r2.ropensci.org/8de3b132a7ee2b128b7957ffe9e334bdee9a8bdd7af93c44b0943d1ef175c3e3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309075150" } ] }