{ "_id": "6a1bdf771d7bb097a0a17d22", "Package": "scanMiR", "Type": "Package", "Title": "scanMiR", "Version": "1.19.0", "Date": "2025-07-24", "Authors@R": "c(\nperson(\"Pierre-Luc\", \"Germain\", email=\"pierre-luc.germain@hest.ethz.ch\",\nrole=c(\"cre\",\"aut\"), comment=c(ORCID=\"0000-0003-3418-4218\")),\nperson(\"Michael\", \"Soutschek\", email=\"michael.soutschek@hest.ethz.ch\", role=\"aut\"),\nperson(\"Fridolin\", \"Gross\", email=\"fridolin.gross@u-bordeaux.fr\", role=\"aut\"))", "Description": "A set of tools for working with miRNA affinity models\n(KdModels), efficiently scanning for miRNA binding sites, and\npredicting target repression. It supports scanning using miRNA\nseeds, full miRNA sequences (enabling 3' alignment) and\nKdModels, and includes the prediction of slicing and TDMD\nsites. Finally, it includes utility and plotting functions\n(e.g. for the visual representation of miRNA-target alignment).", "License": "GPL-3", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "biocViews": "miRNA, SequenceMatching, Alignment", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:30 UTC", "RemoteUrl": "https://github.com/bioc/scanMiR", "RemoteRef": "HEAD", "RemoteSha": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:24:07 UTC", "User": "root" }, "Author": "Pierre-Luc Germain [cre, aut] (ORCID:\n),\nMichael Soutschek [aut],\nFridolin Gross [aut]", "Maintainer": "Pierre-Luc Germain ", "MD5sum": "44e7a91da11af1dee0e11abd7aadb061", "_user": "bioc", "_type": "src", "_file": "scanMiR_1.19.0.tar.gz", "_fileid": "9119b9f74f118729e2b6202ef2993279b20a5d729466088307dd5336e36cd3ea", "_filesize": 797101, "_sha256": "9119b9f74f118729e2b6202ef2993279b20a5d729466088307dd5336e36cd3ea", "_created": "2026-05-31T06:24:07.000Z", "_published": "2026-05-31T07:12:55.770Z", "_jobs": [ { "job": 78705332465, "time": 213, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7314420669" }, { "job": 78705332466, "time": 291, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7314428751" }, { "job": 78705332462, "time": 292, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7314428862" }, { "job": 78705332490, "time": 173, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7314699156" }, { "job": 78705332492, "time": 146, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7314688791" }, { "job": 78705111741, "time": 245, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314397412" }, { "job": 78705332461, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314413681" }, { "job": 78705332494, "time": 179, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7314417468" }, { "job": 78705332491, "time": 183, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7314417878" }, { "job": 78705332489, "time": 193, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7314419008" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/scanMiR", "_commit": { "id": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380990 }, "_maintainer": { "name": "Pierre-Luc Germain", "email": "pierre-luc.germain@hest.ethz.ch", "login": "plger", "orcid": "0000-0003-3418-4218", "description": "like sailors who on the open sea must reconstruct their ship but are never able to start afresh from the bottom...", "uuid": 9786697 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "Biostrings", "role": "Imports" }, { "package": "pwalign", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "seqLogo", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "mirna", "sequencematching", "alignment" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 330, "source": "https://www.bioconductor.org/packages/stats/bioc/scanMiR" }, "_searchresults": 65, "_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/scanMiR.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggregateMatches", "assignKdType", "conservation", "dummyKdData", "findSeedMatches", "get3pAlignment", "get8merRange", "getKdModel", "getKmers", "getMatchTypes", "getRandomSeq", "getSeed8mers", "KdModelList", "plotKdModel", "removeOverlappingRanges", "show", "summary", "viewTargetAlignment" ], "_datasets": [ { "name": "SampleKdModel", "title": "Example KdModel (hsa-miR-155-5p)", "object": "SampleKdModel", "file": "SampleKdModel.RData", "class": [ "KdModel" ], "fields": [], "table": false, "tojson": true }, { "name": "SampleTranscript", "title": "Example transcript sequence", "object": "SampleTranscript", "file": "SampleTranscript.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "aggregateMatches", "title": "aggregateMatches", "topics": [ "aggregateMatches" ] }, { "page": "assignKdType", "title": "assignKdType", "topics": [ "assignKdType" ] }, { "page": "conservation", "title": "conservation", "topics": [ "conservation" ] }, { "page": "dummyKdData", "title": "Create dummy log_kd per 12-mer data", "topics": [ "dummyKdData" ] }, { "page": "findSeedMatches", "title": "Predicting and characterizing miRNA binding sites", "topics": [ "findSeedMatches" ] }, { "page": "get3pAlignment", "title": "Finds 3' complementary binding of a miRNA", "topics": [ "get3pAlignment" ] }, { "page": "get8merRange", "title": "get8merRange", "topics": [ "get8merRange" ] }, { "page": "getKdModel", "title": "getKdModel", "topics": [ "getKdModel" ] }, { "page": "getKmers", "title": "getKmers", "topics": [ "getKmers" ] }, { "page": "getMatchTypes", "title": "getMatchTypes", "topics": [ "getMatchTypes" ] }, { "page": "getRandomSeq", "title": "getRandomSeq", "topics": [ "getRandomSeq" ] }, { "page": "getSeed8mers", "title": "getSeed8mers", "topics": [ "getSeed8mers" ] }, { "page": "KdModel", "title": "miRNA affinity models", "topics": [ "c,KdModel-method", "KdModel", "KdModel-class", "KdModel-methods", "show,KdModel-method", "summary,KdModel-method" ] }, { "page": "KdModelList", "title": "KdModelList", "topics": [ "KdModelList", "KdModelList-class" ] }, { "page": "KdModelList-methods", "title": "Methods for the 'KdModelList' classes", "topics": [ "KdModelList-methods", "KdModelList-methods,KdModelList-method", "summary,KdModelList-method", "[,KdModelList,ANY-method", "[,KdModelList-methods,KdModelList-method" ] }, { "page": "plotKdModel", "title": "plotKdModel", "topics": [ "plotKdModel" ] }, { "page": "removeOverlappingRanges", "title": "removeOverlappingRanges", "topics": [ "removeOverlappingRanges" ] }, { "page": "SampleKdModel", "title": "Example KdModel (hsa-miR-155-5p)", "topics": [ "SampleKdModel" ] }, { "page": "SampleTranscript", "title": "Example transcript sequence", "topics": [ "SampleTranscript" ] }, { "page": "viewTargetAlignment", "title": "viewTargetAlignment", "topics": [ "viewTargetAlignment" ] } ], "_readme": "https://github.com/bioc/scanMiR/raw/HEAD/README.md", "_rundeps": [ "BH", "BiocGenerics", "BiocParallel", "Biostrings", "cli", "codetools", "cowplot", "cpp11", "crayon", "data.table", "farver", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lambda.r", "lifecycle", "pwalign", "R6", "RColorBrewer", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "seqLogo", "snow", "stringi", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "scanning.Rmd", "filename": "scanning.html", "title": "Scanning sequences for miRNA binding sites and exploring matches with scanMiR", "author": "Fridolin Gross, Pierre-Luc Germain, Michael Soutschek", "engine": "knitr::rmarkdown", "headings": [ "Scanning", "Background", "Basic Scan", "Using a miRNA Seed", "Using a miRNA sequence", "Using a KdModel", "About match types", "Further Options", "ORF length", "Supplementary 3' pairing", "Shadow and Overlapping Matches", "Aggregation on the fly", "Aggregating Sites", "Basic Aggregation", "Dealing with very large scans", "Multithreading", "Dealing with large collections of predictions", "Session info" ], "created": "2021-04-13 11:20:57", "modified": "2023-06-08 16:24:20", "commits": 23 }, { "source": "Kdmodels.Rmd", "filename": "Kdmodels.html", "title": "miRNA affinity models and the KdModel class", "author": "Pierre-Luc Germain, Michael Soutschek, Fridolin Gross", "engine": "knitr::rmarkdown", "headings": [ "12-mer dissociation rates", "KdModels", "KdModelLists", "Creating a KdModel object", "Common KdModel collections", "Under the hood", "Session info" ], "created": "2021-04-13 11:20:57", "modified": "2024-04-15 18:19:40", "commits": 9 } ], "_score": 5.76715586608218, "_indexed": true, "_nocasepkg": "scanmir", "_universes": [ "bioc", "plger" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-05-31T06:27:58.000Z", "distro": "noble", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "06b7c10f4691bcfb24a690a193f7da517dafb97515cd3fff0cf00ad845749289", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-05-31T06:28:02.000Z", "distro": "noble", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "4d6f17b47c3d8096aa3a3e089984562db2e98b65d50f216051b884c15b726de0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-05-31T07:11:28.000Z", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "d9523bedaebda298c9ddeed047908a24ad06e76c547110359e4fa2bba7cda856", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-05-31T07:10:02.000Z", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "08516b8bd675005131c612a5fc67317a7f854bc1220ef6866851c706d58a4dd4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-05-31T06:26:54.000Z", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "c682124ee2236f1baa207d9265ec40dc10756720bb8ec0dd1d7bc006a6cb6b3d", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-05-31T06:26:06.000Z", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "a178f4d93eeec5d92d5cbefa5e1d3b2fe3c9f13109faf7c3a5ff3b9a27e25dbb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-05-31T06:26:06.000Z", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "7e4eaa0ad2a7aea05526aad4997fbec0d82a895dbba4e105ce79891023895b86", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" }, { "r": "4.6.0", "os": "win", "version": "1.19.0", "date": "2026-05-31T06:26:19.000Z", "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c", "fileid": "2b8802c9e4ff08d0abb9fb9fba0c350f033a17e32a9b567cce8def789a0427e5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705226429" } ] }