{ "_id": "6a1af7b01d7bb097a09fa8ce", "Package": "similaRpeak", "Type": "Package", "Title": "Metrics to estimate a level of similarity between two ChIP-Seq\nprofiles", "Version": "1.45.0", "Date": "2014-08-08", "Authors@R": "c( person(\"Astrid\",\"Deschênes\",\nemail=\"adeschen@hotmail.com\",\nrole=c(\"cre\",\"aut\")), person(\"Elsa\", \"Bernatchez\",\nemail=\"elsa.bernatchez.1@ulaval.ca\", role=c(\"aut\")),\nperson(\"Charles\", \"Joly Beauparlant\",\nemail=\"charles.joly-beauparlant@crchul.ulaval.ca\",\nrole=c(\"aut\")), person(\"Fabien Claude\", \"Lamaze\",\nemail=\"fabien.lamaze.1@ulaval.ca\", role=c(\"aut\")),\nperson(\"Rawane\", \"Samb\", email=\"rawane.samb.1@ulaval.ca\",\nrole=c(\"aut\")), person(\"Pascal\", \"Belleau\",\nemail=\"pascal_belleau@hotmail.com\", role=c(\"aut\")),\nperson(\"Arnaud\", \"Droit\",\nemail=\"arnaud.droit@crchuq.ulaval.ca\", role=c(\"aut\")))", "Description": "This package calculates metrics which quantify the level\nof similarity between ChIP-Seq profiles. More specifically, the\npackage implements six pseudometrics specialized in pattern\nsimilarity detection in ChIP-Seq profiles.", "biocViews": "BiologicalQuestion, ChIPSeq, Genetics, MultipleComparison,\nDifferentialExpression", "License": "Artistic-2.0", "URL": "https://github.com/adeschen/similaRpeak", "BugReports": "https://github.com/adeschen/similaRpeak/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "NeedsCompilation": "no", "RoxygenNote": "6.0.1", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:16 UTC", "RemoteUrl": "https://github.com/bioc/similaRpeak", "RemoteRef": "HEAD", "RemoteSha": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "Packaged": { "Date": "2026-05-30 09:48:25 UTC", "User": "root" }, "Author": "Astrid Deschênes [cre, aut],\nElsa Bernatchez [aut],\nCharles Joly Beauparlant [aut],\nFabien Claude Lamaze [aut],\nRawane Samb [aut],\nPascal Belleau [aut],\nArnaud Droit [aut]", "Maintainer": "Astrid Deschênes ", "MD5sum": "81fa537fde4c9771578df689ecb98579", "_user": "bioc", "_type": "src", "_file": "similaRpeak_1.45.0.tar.gz", "_fileid": "6c0b4e8a753f5298128202686fc29e004050460a91fdf1ee42dcf4ee15385503", "_filesize": 2102268, "_sha256": "6c0b4e8a753f5298128202686fc29e004050460a91fdf1ee42dcf4ee15385503", "_created": "2026-05-30T09:48:25.000Z", "_published": "2026-05-30T14:44:00.215Z", "_jobs": [ { "job": 78640683093, "time": 156, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307502583" }, { "job": 78640683091, "time": 241, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307509742" }, { "job": 78640683094, "time": 192, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307505753" }, { "job": 78640683090, "time": 92, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308962630" }, { "job": 78640683087, "time": 120, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308965499" }, { "job": 78639936756, "time": 274, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307297871" }, { "job": 78640683082, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307500487" }, { "job": 78640683097, "time": 97, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307495313" }, { "job": 78640683083, "time": 105, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307495802" }, { "job": 78640683092, "time": 104, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307498008" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/similaRpeak", "_commit": { "id": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380076 }, "_maintainer": { "name": "Astrid Deschênes", "email": "adeschen@hotmail.com", "login": "adeschen", "description": "I am a Computational Science Analyst at Cold Spring Harbor Laboratory. ", "uuid": 7254636 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R6", "version": ">= 2.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "GenomicAlignments", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "biologicalquestion", "chipseq", "genetics", "multiplecomparison", "differentialexpression", "bioconductor", "bioconductor-package", "chip-profiles", "chip-seq", "metrics" ], "_stars": 7, "_contributors": [ { "user": "adeschen", "count": 247, "uuid": 7254636 }, { "user": "elsabernatchez", "count": 17, "uuid": 8430937 }, { "user": "nturaga", "count": 12, "uuid": 2746443 }, { "user": "dtenenba", "count": 8, "uuid": 2286826 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "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": 424, "source": "https://www.bioconductor.org/packages/stats/bioc/similaRpeak" }, "_mentions": 1, "_devurl": "https://github.com/adeschen/similarpeak", "_searchresults": 17, "_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/readme.html", "extra/readme.md", "extra/similaRpeak.html", "manual.pdf" ], "_homeurl": "https://github.com/adeschen/similarpeak", "_realowner": "bioc", "_cranurl": false, "_exports": [ "MetricFactory", "similarity" ], "_datasets": [ { "name": "chr7Profiles", "title": "ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)", "object": "chr7Profiles", "file": "chr7Profiles.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "demoProfiles", "title": "ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)", "object": "demoProfiles", "file": "demoProfiles.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "similaRpeak-package", "title": "similaRpeak: Metrics to estimate a level of similarity between two ChIP-Seq profiles", "topics": [ "similaRpeak-package", "similaRpeak" ] }, { "page": "chr7Profiles", "title": "ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)", "topics": [ "chr7Profiles" ] }, { "page": "demoProfiles", "title": "ChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)", "topics": [ "demoProfiles" ] }, { "page": "DiffPosMax", "title": "DiffPosMax class", "topics": [ "DiffPosMax" ] }, { "page": "diffPosMaxMethod", "title": "Difference between two profiles maximal peaks positions", "topics": [ "diffPosMaxMethod" ] }, { "page": "Metric", "title": "Metric class", "topics": [ "Metric" ] }, { "page": "MetricFactory", "title": "MetricFactory object", "topics": [ "MetricFactory" ] }, { "page": "RatioArea", "title": "RatioArea class", "topics": [ "RatioArea" ] }, { "page": "ratioAreaMethod", "title": "Ratio of profiles area between two profiles", "topics": [ "ratioAreaMethod" ] }, { "page": "RatioIntersect", "title": "RatioIntersect class", "topics": [ "RatioIntersect" ] }, { "page": "ratioIntersectMethod", "title": "Ratio between the intersection area of two profiles and the total area covered by those profiles", "topics": [ "ratioIntersectMethod" ] }, { "page": "RatioMaxMax", "title": "RatioMaxMax class", "topics": [ "RatioMaxMax" ] }, { "page": "ratioMaxMaxMethod", "title": "Ratio of profiles maximal peaks between two profiles", "topics": [ "ratioMaxMaxMethod" ] }, { "page": "RatioNormalizedIntersect", "title": "RatioNormalizedIntersect class", "topics": [ "RatioNormalizedIntersect" ] }, { "page": "similarity", "title": "Calculate metrics which estimate the level of similarity between two ChIP-Seq profiles", "topics": [ "similarity" ] }, { "page": "SpearmanCorrelation", "title": "SpearmanCorrelation class", "topics": [ "SpearmanCorrelation" ] }, { "page": "spearmanCorrMethod", "title": "Spearman's rho statistic of two profiles", "topics": [ "spearmanCorrMethod" ] } ], "_readme": "https://github.com/bioc/similaRpeak/raw/HEAD/README.md", "_rundeps": [ "R6" ], "_vignettes": [ { "source": "similaRpeak.Rmd", "filename": "similaRpeak.html", "title": "Similarity between two ChIP-Seq profiles", "engine": "knitr::rmarkdown", "headings": [ "Metrics which estimate similarity between two ChIP-Seq profiles", "Introduction", "Loading the similaRpeak package", "Inputs", "ChIP-Seq profiles vectors", "Metrics", "Metric versus Pseudometric", "Metrics Presentation", "RATIO_AREA", "DIFF_POS_MAX", "RATIO_MAX_MAX", "RATIO_INTERSECT", "RATIO_NORMALIZED_INTERSECT", "SPEARMAN_CORRELATION", "Using similaRpeak on real ChIP-Seq profiles", "Metrics calculation using a MetricFactory object", "Session info", "References" ], "created": "2015-04-10 23:33:14", "modified": "2017-04-01 00:32:30", "commits": 4 } ], "_score": 5.853698211776175, "_indexed": true, "_nocasepkg": "similarpeak", "_universes": [ "bioc", "adeschen" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.0", "date": "2026-05-30T10:27:18.000Z", "distro": "noble", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "e76dbaa57a10ef182d6f927b481e1b99a0b5ab7820f06cea394f9d9a1d93a578", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" }, { "r": "4.6.0", "os": "linux", "version": "1.45.0", "date": "2026-05-30T10:26:30.000Z", "distro": "noble", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "2ea05bee01b20622e0a87d295b99ea03e28e4b2695d10bbf609d27c65ae7baa4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" }, { "r": "4.5.3", "os": "mac", "version": "1.45.0", "date": "2026-05-30T14:43:04.000Z", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "11bd143b2be33fb9774dfe38aa5aaeeef18f7dcb15e105338c9868b046e14f1f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" }, { "r": "4.6.0", "os": "mac", "version": "1.45.0", "date": "2026-05-30T14:43:25.000Z", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "87376d21ece53e9b419dd7f04bed60d4355d832a001bac70a5132eb86ad3a896", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" }, { "r": "4.6.0", "os": "wasm", "version": "1.45.0", "date": "2026-05-30T10:25:42.000Z", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "0e964a75147d822b79900b1e4d2f77481efff2397907afb78620b898cf8f02ca", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" }, { "r": "4.7.0", "os": "win", "version": "1.45.0", "date": "2026-05-30T10:24:18.000Z", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "5d9659c6610e826ad049424528994cfccee54cd9d5a338cfd07e75b3ac898bf8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" }, { "r": "4.5.3", "os": "win", "version": "1.45.0", "date": "2026-05-30T10:24:25.000Z", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "6f46d9801491041304c92984b912585cb444a765d7b54a63c00cba66df39cc16", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" }, { "r": "4.6.0", "os": "win", "version": "1.45.0", "date": "2026-05-30T10:24:53.000Z", "commit": "20d8eb7b4c6705f4ee7d86b5d86e18d8c65d59bb", "fileid": "f65d180a3402aaa8fe071091bdcfb0e350958b2d194594e4d1c1786313813c7c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677069082" } ] }