{ "_id": "6a1bd29f1d7bb097a0a148de", "Package": "RNAmodR.RiboMethSeq", "Type": "Package", "Title": "Detection of 2'-O methylations by RiboMethSeq", "Version": "1.27.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:50:23 UTC", "RemoteUrl": "https://github.com/bioc/RNAmodR.RiboMethSeq", "RemoteRef": "HEAD", "RemoteSha": "6f2e7546b9505068b7c496709d1e2c80c749991e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 06:58:39 UTC", "User": "root" }, "Author": "Felix G.M. Ernst [aut, cre] (ORCID:\n),\nDenis L.J. Lafontaine [ctb, fnd]", "Maintainer": "Felix G.M. Ernst ", "MD5sum": "c91cab79f3e7ab620a14f2c553944098", "_user": "bioc", "_type": "src", "_file": "RNAmodR.RiboMethSeq_1.27.0.tar.gz", "_fileid": "fe1254c0834fd86494e11154a7e8132fa9d22273199072d9f362871a5b0c551b", "_filesize": 457768, "_sha256": "fe1254c0834fd86494e11154a7e8132fa9d22273199072d9f362871a5b0c551b", "_created": "2026-05-30T06:58:39.000Z", "_published": "2026-05-31T06:18:07.902Z", "_jobs": [ { "job": 78703911025, "time": 253, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306299667" }, { "job": 78703911043, "time": 632, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306343980" }, { "job": 78703911144, "time": 602, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306340387" }, { "job": 78703911049, "time": 376, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307113467" }, { "job": 78703910955, "time": 414, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7314356234" }, { "job": 78703910939, "time": 392, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306268813" }, { "job": 78703911039, "time": 304, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306305615" }, { "job": 78703911068, "time": 895, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306374454" }, { "job": 78703911146, "time": 753, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306357928" }, { "job": 78703911052, "time": 781, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306361013" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RNAmodR.RiboMethSeq", "_commit": { "id": "6f2e7546b9505068b7c496709d1e2c80c749991e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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": true, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_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": 4, "_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/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "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": true, "_nocasepkg": "rnamodr.ribomethseq", "_universes": [ "bioc", "felixernst" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-05-30T07:04:16.000Z", "distro": "noble", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "f2af5b32e52649fdbba7831909390bf99f5f6df552a52cf50d9b98815f48bb41", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" }, { "r": "4.6.0", "os": "linux", "version": "1.27.0", "date": "2026-05-30T07:04:07.000Z", "distro": "noble", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "4371f22118f19d191f7ad312a38125f54d1887593be45d31ef71199ce83b4fb2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-05-30T09:13:04.000Z", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "40a3b46cc137edf65693c2bd5d45335f49ca4d67836c4031e3abeb1b963551f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" }, { "r": "4.6.0", "os": "mac", "version": "1.27.0", "date": "2026-05-31T06:12:43.000Z", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "cbe4ba765f351e99ba4e05cf280095e3a4a6bd4afff1216966964e171d7677bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-05-30T07:04:36.000Z", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "15cc231226829a2862e334a1fc620443561acbe887c8609dd8ca0b7380e40bec", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-05-30T07:06:28.000Z", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "1b3aa82dbf713dbfdd18c6e7df09f2358ecb5f5208abb6bb02c726c8603d0115", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-05-30T07:05:37.000Z", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "5cd8b938a53fceb7737ee64ea96f542ba95e8247af16f1d1ad05b4c38a242d78", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" }, { "r": "4.6.0", "os": "win", "version": "1.27.0", "date": "2026-05-30T07:05:51.000Z", "commit": "6f2e7546b9505068b7c496709d1e2c80c749991e", "fileid": "27ae6b45ac48a6ed45ef736583db879eba8ad6c28fd77bb01fcbefa74c97ceee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677367524" } ] }