{
  "_id": "6a1b0df61d7bb097a0a08eaa",
  "Package": "RNAmodR.RiboMethSeq",
  "Type": "Package",
  "Title": "Detection of 2'-O methylations by RiboMethSeq",
  "Version": "1.26.0",
  "Date": "2025-09-25",
  "Authors@R": "c(person(\"Felix G.M.\", \n\"Ernst\",\nemail = \"felix.gm.ernst@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5064-0928\")),\nperson(\"Denis L.J.\",\n\"Lafontaine\",\nemail = \"denis.lafontaine@ulb.ac.be\",\nrole = c(\"ctb\", \"fnd\")))",
  "Description": "RNAmodR.RiboMethSeq implements the detection of 2'-O\nmethylations on RNA from experimental data generated with the\nRiboMethSeq protocol. The package builds on the core\nfunctionality of the RNAmodR package to detect specific\npatterns of the modifications in high throughput sequencing\ndata.",
  "biocViews": "Software, WorkflowStep, Visualization, Sequencing",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "Collate": "'RNAmodR.RiboMethSeq.R' 'Modifier-RiboMethSeq-class.R'\n'Modifier-RiboMethSeq-viz.R'",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "BugReports": "https://github.com/FelixErnst/RNAmodR.RiboMethSeq/issues",
  "URL": "https://github.com/FelixErnst/RNAmodR.RiboMethSeq",
  "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:23 UTC",
  "RemoteUrl": "https://github.com/bioc/RNAmodR.RiboMethSeq",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 11:03:13 UTC",
    "User": "root"
  },
  "Author": "Felix G.M. Ernst [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5064-0928>),\nDenis L.J. Lafontaine [ctb, fnd]",
  "Maintainer": "Felix G.M. Ernst <felix.gm.ernst@outlook.com>",
  "MD5sum": "8702176c26f562d55e55e57f6117336d",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "RNAmodR.RiboMethSeq_1.26.0.tar.gz",
  "_fileid": "e043df56f059f26a16d13f228d89190d4dd2cdf780639d28dd2acc94382f84df",
  "_filesize": 457849,
  "_sha256": "e043df56f059f26a16d13f228d89190d4dd2cdf780639d28dd2acc94382f84df",
  "_created": "2026-05-30T11:03:13.000Z",
  "_published": "2026-05-30T16:19:02.736Z",
  "_jobs": [
    {
      "job": 78644438728,
      "time": 273,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307803045"
    },
    {
      "job": 78644438780,
      "time": 562,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307827125"
    },
    {
      "job": 78644438739,
      "time": 638,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307833832"
    },
    {
      "job": 78644438726,
      "time": 380,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309563730"
    },
    {
      "job": 78644438723,
      "time": 326,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309558646"
    },
    {
      "job": 78643923587,
      "time": 387,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307719268"
    },
    {
      "job": 78644438720,
      "time": 231,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307798674"
    },
    {
      "job": 78644438759,
      "time": 795,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307847284"
    },
    {
      "job": 78644438774,
      "time": 754,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307843841"
    },
    {
      "job": 78644438752,
      "time": 713,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307840715"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/RNAmodR.RiboMethSeq",
  "_commit": {
    "id": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380623
  },
  "_maintainer": {
    "name": "Felix G.M. Ernst",
    "email": "felix.gm.ernst@outlook.com",
    "login": "felixernst",
    "description": "",
    "uuid": 17824332,
    "orcid": "0000-0001-5064-0928"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "RNAmodR",
      "version": ">= 1.5.3",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "Gviz",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "Seqinfo",
      "role": "Suggests"
    },
    {
      "package": "RNAmodR.Data",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-39",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "workflowstep",
    "visualization",
    "sequencing",
    "bioconductor",
    "modifications",
    "ribomethseq",
    "rna",
    "rnamodr"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "felixernst",
      "count": 76,
      "uuid": 17824332
    },
    {
      "user": "nturaga",
      "count": 12,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 12,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 315,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RNAmodR.RiboMethSeq"
  },
  "_devurl": "https://github.com/felixernst/rnamodr.ribomethseq",
  "_searchresults": 7,
  "_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/RNAmodR.RiboMethSeq.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/felixernst/rnamodr.ribomethseq",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aggregateData",
    "findMod",
    "getDataTrack",
    "ModRiboMethSeq",
    "ModSetRiboMethSeq",
    "plotData",
    "plotDataByCoord",
    "settings<-"
  ],
  "_datasets": [
    {
      "name": "msrms",
      "title": "Example data in the RNAmodR.RiboMethSeq package",
      "object": "msrms",
      "file": "msrms.rda",
      "class": [
        "ModSetRiboMethSeq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ModRiboMethSeq",
      "title": "ModRiboMethSeq class to analyze RiboMethSeq data",
      "topics": [
        "ModRiboMethSeq",
        "ModRiboMethSeq-class",
        "ModSetRiboMethSeq",
        "ModSetRiboMethSeq-class",
        "RiboMethSeq"
      ]
    },
    {
      "page": "ModRiboMethSeq-functions",
      "title": "Functions for ModRiboMethSeq",
      "topics": [
        "aggregate",
        "aggregateData,ModRiboMethSeq-method",
        "findMod,ModRiboMethSeq-method",
        "getDataTrack,ModRiboMethSeq-method",
        "modify",
        "ModRiboMethSeq-functions",
        "plotData",
        "plotData,ModRiboMethSeq-method",
        "plotData,ModSetRiboMethSeq-method",
        "plotDataByCoord",
        "plotDataByCoord,ModRiboMethSeq,GRanges-method",
        "plotDataByCoord,ModSetRiboMethSeq,GRanges-method",
        "settings",
        "settings<-,ModRiboMethSeq-method"
      ]
    },
    {
      "page": "RNAmodR.RiboMethSeq",
      "title": "RNAmodR.RiboMethSeq",
      "topics": [
        "RNAmodR.RiboMethSeq"
      ]
    },
    {
      "page": "RNAmodR.RiboMethSeq-datasets",
      "title": "Example data in the RNAmodR.RiboMethSeq package",
      "topics": [
        "msrms",
        "RNAmodR.RiboMethSeq-datasets"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/RNAmodR.RiboMethSeq/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationFilter",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "biovizBase",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "bslib",
    "cachem",
    "caTools",
    "checkmate",
    "cigarillo",
    "cli",
    "cluster",
    "codetools",
    "colorRamps",
    "colorspace",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "deldir",
    "dichromat",
    "digest",
    "dplyr",
    "ensembldb",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gplots",
    "gridExtra",
    "gtable",
    "gtools",
    "Gviz",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "interp",
    "IRanges",
    "isoband",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "latticeExtra",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "Modstrings",
    "nnet",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "ProtGenerics",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RCurl",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "RNAmodR",
    "ROCR",
    "rpart",
    "Rsamtools",
    "RSQLite",
    "rstudioapi",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "txdbmaker",
    "UCSC.utils",
    "utf8",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "RNAmodR.RiboMethSeq.Rmd",
      "filename": "RNAmodR.RiboMethSeq.html",
      "title": "RNAmodR: RiboMethSeq",
      "author": "Felix G.M. Ernst and Denis L.J. Lafontaine",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Example workflow",
        "Analysis of data",
        "Visualizing the results",
        "Session info",
        "References"
      ],
      "created": "2019-01-15 14:19:51",
      "modified": "2020-01-09 12:19:19",
      "commits": 20
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": false,
  "_nocasepkg": "rnamodr.ribomethseq",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/RNAmodR.RiboMethSeq",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.26.0",
      "date": "2026-05-30T11:18:55.000Z",
      "distro": "noble",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "760c305c91fb8d21973b9756ced42d6ef4c45325637f4cb05dc4c8be8724c930",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.26.0",
      "date": "2026-05-30T11:20:12.000Z",
      "distro": "noble",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "510ae9e98cd37931104b762aee657846c730e3d8d9c0c5b9750c2fed351cb82b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.26.0",
      "date": "2026-05-30T16:14:29.000Z",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "4ece9d97d38589e23cd4093612a6d6d8d299c15c1f72cb2a506cd867503ab0c9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.26.0",
      "date": "2026-05-30T16:14:18.000Z",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "97f9ce2921a019676edc0e11a4065626753d6936939b8d5dc9d088e8cb2c996e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.26.0",
      "date": "2026-05-30T11:18:55.000Z",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "581c781fef500d9daf5d931d587dc29cb284efe036d56974c5e4ed7759ebe21c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.26.0",
      "date": "2026-05-30T11:22:30.000Z",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "b3e9479fec5f78a0c56fb2c51e8730dbca1b5c6e9142d282f238011b8cdbeb19",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.26.0",
      "date": "2026-05-30T11:21:37.000Z",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "898c4184144436699a165957644a1ab4955eb0d704e44c0d9d53a075070e0ee2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.26.0",
      "date": "2026-05-30T11:21:09.000Z",
      "commit": "bd74cb45db01ac034746a2b7a5df1f1c202fae3c",
      "fileid": "6c3e829f7293756dea07fb9639904426c5cbe9715f492a7c6c452e7299003ed2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681220225"
    }
  ]
}