{
  "_id": "6a494670a788432aeabf3775",
  "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": "2026-07-04 15:05:33 UTC",
    "User": "root"
  },
  "Author": "Pierre-Luc Germain [cre, aut] (ORCID:\n<https://orcid.org/0000-0003-3418-4218>),\nMichael Soutschek [aut],\nFridolin Gross [aut]",
  "Maintainer": "Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch>",
  "_user": "bioc",
  "_type": "src",
  "_file": "scanMiR_1.19.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/01c646720f7dd9b9d4e867010b07ce795653b1de2d7c17b6b74410196071e192",
  "_filesize": 801167,
  "_sha256": "01c646720f7dd9b9d4e867010b07ce795653b1de2d7c17b6b74410196071e192",
  "_expires": "2026-10-12T17:44:15.000Z",
  "_created": "2026-07-04T15:05:33.000Z",
  "_published": "2026-07-04T17:44:16.641Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900",
  "_status": "success",
  "_upstream": "https://github.com/bioc/scanMiR",
  "_commit": {
    "id": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "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": "resolute",
  "_jobs": [
    {
      "job": 85153300500,
      "time": 181,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8082828703"
    },
    {
      "job": 85153300651,
      "time": 240,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8082835741"
    },
    {
      "job": 85153300634,
      "time": 290,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082841862"
    },
    {
      "job": 85153300626,
      "time": 132,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8082822996"
    },
    {
      "job": 85153300644,
      "time": 130,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082822710"
    },
    {
      "job": 85153300352,
      "time": 222,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8082806378"
    },
    {
      "job": 85153300530,
      "time": 135,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8082823287"
    },
    {
      "job": 85153300643,
      "time": 195,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8082830389"
    },
    {
      "job": 85153300712,
      "time": 167,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8082827136"
    },
    {
      "job": 85153300696,
      "time": 178,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082828292"
    }
  ],
  "_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",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_searchresults": 67,
  "_rbuild": "4.6.1",
  "_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",
    "LICENSE",
    "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": 5.780317312140151,
  "_indexed": true,
  "_nocasepkg": "scanmir",
  "_universes": [
    "bioc",
    "plger"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-07-04T15:08:37.000Z",
      "distro": "resolute",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/dcda1d19a1fa356c79e456b3926371a6dede2f8fcf6fa47e39f0d83f1e227695",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-07-04T15:09:31.000Z",
      "distro": "resolute",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/c06000703ef3f5237de2bff743885dc69e634820b0c99c3d42b095afcadd581a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-07-04T15:07:22.000Z",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/f13c1b9e939d0e4f9600bca3c3ee9172a75eb3302cf027c632083190e3ce7eb8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-07-04T15:07:19.000Z",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/8d7a03c6342e67c1d312f2f43047c66f19e78172b92a805a0d7c92eeb4cd328e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.19.0",
      "date": "2026-07-04T15:08:14.000Z",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/d127fef4bbd1c5fea942b374eb76eff089d020576a9bc5df1a086d3b6504d852",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-07-04T15:07:40.000Z",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/02469f76cee50bbcf79a19f029a1c67c1d808667ee0948387d796084642dce14",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-07-04T15:07:21.000Z",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/828772f25776185ba96aa56abe4fc6fe711ebd9602c120027128ab16cb345bdb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-07-04T15:07:31.000Z",
      "commit": "a482f71c94fea7a3c8348bc7cbcfd06f6a3ea75c",
      "fileid": "https://r2.ropensci.org/a79d174aafabfaf6aebad0b34e6200e821d3260033dc995d4d7bb4f8ddf5eee8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28710136900"
    }
  ]
}