{ "_id": "6a4940ed18cdde069385dda7", "Package": "Modstrings", "Type": "Package", "Title": "Working with modified nucleotide sequences", "Version": "1.29.0", "Date": "2022-12-24", "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": "Representing nucleotide modifications in a nucleotide\nsequence is usually done via special characters from a number\nof sources. This represents a challenge to work with in R and\nthe Biostrings package. The Modstrings package implements this\nfunctionallity for RNA and DNA sequences containing modified\nnucleotides by translating the character internally in order to\nwork with the infrastructure of the Biostrings package. For\nthis the ModRNAString and ModDNAString classes and derivates\nand functions to construct and modify these objects despite the\nencoding issues are implemenented. In addition the conversion\nfrom sequences to list like location information (and the\nreverse operation) is implemented as well.", "License": "Artistic-2.0", "Encoding": "UTF-8", "biocViews": "DataImport, DataRepresentation, Infrastructure, Sequencing,\nSoftware", "Collate": "'Modstrings.R' 'AllGenerics.R'\n'Modstrings-external-functions.R'\n'Modstrings-external-C-calls.R' 'Modstrings-ModStringCodec.R'\n'Modstrings-ModString.R' 'Modstrings-ModStringSet.R'\n'Modstrings-ModStringViews.R' 'Modstrings-MaskedModString.R'\n'Modstrings-ModStringCodec-data.R'\n'Modstrings-ModStringSet-io.R' 'Modstrings-ModStringSetList.R'\n'Modstrings-QualityScaledModStringSet.R'\n'Modstrings-letterFrequency.R' 'Modstrings-modifyNucleotide.R'\n'Modstrings-replaceLetterAt.R' 'Modstrings-sanitize.R'\n'Modstrings-separate.R' 'Modstrings-seqtype.R' 'datasets.R'\n'utils.R' 'zzz.R'", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "BugReports": "https://github.com/FelixErnst/Modstrings/issues", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:49:42 UTC", "RemoteUrl": "https://github.com/bioc/Modstrings", "RemoteRef": "HEAD", "RemoteSha": "4509228b0af0b505d0a14a5f87fa28996a89f553", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 07:02:55 UTC", "User": "root" }, "Author": "Felix G.M. Ernst [aut, cre] (ORCID:\n),\nDenis L.J. Lafontaine [ctb, fnd]", "Maintainer": "Felix G.M. Ernst ", "_user": "bioc", "_type": "src", "_file": "Modstrings_1.29.0.tar.gz", "_fileid": "https://r2.ropensci.org/dfdcec81e8ea7947b40812f03ee00144c7fe0612ad550ffced5fb135dd8ac391", "_filesize": 264544, "_sha256": "dfdcec81e8ea7947b40812f03ee00144c7fe0612ad550ffced5fb135dd8ac391", "_expires": "2026-10-12T17:20:44.000Z", "_created": "2026-07-04T07:02:55.000Z", "_published": "2026-07-04T17:20:45.619Z", "_bioccheck": { "error": 0, "warning": 1, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28698442034", "_status": "success", "_upstream": "https://github.com/bioc/Modstrings", "_commit": { "id": "4509228b0af0b505d0a14a5f87fa28996a89f553", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380582 }, "_maintainer": { "name": "Felix G.M. Ernst", "email": "felix.gm.ernst@outlook.com", "login": "felixernst", "description": "", "uuid": 17824332, "orcid": "0000-0001-5064-0928" }, "_distro": "resolute", "_jobs": [ { "job": 85151703571, "time": 172, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8079416669" }, { "job": 85151703557, "time": 251, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8079428457" }, { "job": 85151703569, "time": 230, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8079425380" }, { "job": 85151703442, "time": 120, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8079861573" }, { "job": 85151703440, "time": 165, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8079851621" }, { "job": 85151703444, "time": 223, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8079390584" }, { "job": 85151703397, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": 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"letterFrequency", "ModDNAString", "ModDNAStringSet", "ModDNAStringSetList", "modifyNucleotides", "ModRNAString", "ModRNAStringSet", "ModRNAStringSetList", "nomenclature", "QualityScaledModDNAStringSet", "QualityScaledModRNAStringSet", "readModDNAStringSet", "readModRNAStringSet", "readQualityScaledModDNAStringSet", "readQualityScaledModRNAStringSet", "removeIncompatibleModifications", "replaceLetterAt", "sanitizeFromModomics", "sanitizeFromtRNAdb", "sanitizeInput", "separate", "seqtype", "seqtype<-", "shortName", "Views", "writeModStringSet", "writeQualityScaledModStringSet", "XString", "XStringSet" ], "_datasets": [ { "name": "MOD_RNA_DICT_MODOMICS", "title": "Modstrings internals", "object": "MOD_RNA_DICT_MODOMICS", "file": "MOD_RNA_DICT_MODOMICS.rda", "class": [ "DFrame" ], "fields": [], "table": false, "tojson": false }, { "name": "MOD_RNA_DICT_TRNADB", "title": "Modstrings internals", "object": "MOD_RNA_DICT_TRNADB", "file": "MOD_RNA_DICT_TRNADB.rda", "class": [ "DFrame" ], "fields": [], "table": false, "tojson": false }, { "name": "modsDNA", "title": "Modstrings internals", "object": "modsDNA", "file": "modsDNA.rda", "class": [ "DFrame" ], "fields": [], "table": false, "tojson": false }, { "name": "modsRNA", "title": "Modstrings internals", "object": "modsRNA", "file": "modsRNA.rda", "class": [ "DFrame" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "letterFrequency", "title": "Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences", "topics": [ "alphabetFrequency", "alphabetFrequency,MaskedModString-method", "alphabetFrequency,ModDNAString-method", "alphabetFrequency,ModDNAStringSet-method", "alphabetFrequency,ModRNAString-method", "alphabetFrequency,ModRNAStringSet-method", "consensusMatrix,ModStringSet-method", "consensusString", "consensusString,ModDNAStringSet-method", "consensusString,ModRNAStringSet-method", "consensusString,ModStringViews-method", 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"ModRNAStringSetList", "ModRNAStringSetList-class", "ModStringSetList" ] }, { "page": "ModStringViews", "title": "The ModStringViews class extending the XStringViews class", "topics": [ "==,ModStringViews,ModStringViews-method", "==,ModStringViews,XString-method", "==,XStringViews,ModString-method", "ModStringSet,ModStringViews-method", "ModStringViews", "show,ModStringViews-method", "Views,ModString-method" ] }, { "page": "QualityScaledModStringSet", "title": "QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects", "topics": [ "QualityScaledModDNAStringSet", "QualityScaledModDNAStringSet-class", "QualityScaledModRNAStringSet", "QualityScaledModRNAStringSet-class", "QualityScaledModStringSet", "readQualityScaledModDNAStringSet", "readQualityScaledModRNAStringSet", "show,QualityScaledModStringSet-method", "writeQualityScaledModStringSet" ] }, { "page": "replaceLetterAt", "title": "Replacing letters in a nucleotide sequence (or set of nucleotide sequences) at some 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