{ "_id": "6a1adc411d7bb097a09e99ea", "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": "2026-05-30 09:13:05 UTC", "User": "root" }, "Author": "Felix G.M. Ernst [aut, cre] (ORCID:\n),\nDenis L.J. Lafontaine [ctb, fnd]", "Maintainer": "Felix G.M. Ernst ", "MD5sum": "e7fbf3b3251a8789fc7cbf24d4903c07", "_user": "bioc", "_type": "src", "_file": "Modstrings_1.29.0.tar.gz", "_fileid": "01c1fcd269730d4e11d46680ef2550e2f239faf8da87da696b61a01211e74125", "_filesize": 262532, "_sha256": "01c1fcd269730d4e11d46680ef2550e2f239faf8da87da696b61a01211e74125", "_created": "2026-05-30T09:13:05.000Z", "_published": "2026-05-30T12:46:57.289Z", "_jobs": [ { "job": 78638913583, "time": 170, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307135523" }, { "job": 78638913580, "time": 234, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307141484" }, { "job": 78638913615, "time": 271, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307145080" }, { "job": 78638913584, "time": 141, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308281538" }, { "job": 78638913621, "time": 133, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308281688" }, { "job": 78638708795, "time": 210, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307093601" }, { "job": 78638913596, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307130945" }, { "job": 78638913593, "time": 183, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307137108" }, { "job": 78638913600, "time": 166, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307135394" }, { "job": 78638913625, "time": 149, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307133495" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399", "_status": "success", "_host": "GitHub-Actions", "_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": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Biostrings", "version": ">= 2.79.3", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "XVector", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 8, "_updates": [ { "week": "2025-39", "n": 3 }, { "week": "2025-44", "n": 2 }, { "week": "2025-51", "n": 1 }, { "week": "2025-52", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "dataimport", "datarepresentation", "infrastructure", "sequencing", "software", "bioconductor", "biostrings", "dna", "dna-modifications", "modified-nucleotides", "nucleotides", "rna", "rna-modification-alphabet", "rna-modifications", "sequences" ], "_stars": 2, "_contributors": [ { "user": "felixernst", "count": 142, "uuid": 17824332 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 478, "source": "https://www.bioconductor.org/packages/stats/bioc/Modstrings" }, "_devurl": "https://github.com/felixernst/modstrings", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/Modstrings.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/felixernst/modstrings", "_realowner": "bioc", "_cranurl": false, "_exports": [ "alphabet", "alphabetFrequency", "combineIntoModstrings", "combineModifications", "consensusMatrix", "consensusString", "fullName", "hasOnlyBaseLetters", "incompatibleModifications", "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", "hasOnlyBaseLetters", "hasOnlyBaseLetters,ModDNAString-method", "hasOnlyBaseLetters,ModDNAStringSet-method", "hasOnlyBaseLetters,ModRNAString-method", "hasOnlyBaseLetters,ModRNAStringSet-method", "letterFrequency", "letterFrequency,MaskedModString-method", "letterFrequency,ModStringViews-method", "letterFrequencyInSlidingView" ] }, { "page": "MaskedModString", "title": "MaskedModString objects", "topics": [ "MaskedModString", "seqtype,MaskedModString-method" ] }, { "page": "ModDNAString", "title": "ModDNAString class", "topics": [ "ModDNAString" ] }, { "page": "modifyNucleotides", "title": "Modifying nucleotides in a nucleotide sequence (or set of sequences) at specified locations", "topics": [ "modifyNucleotides", "modifyNucleotides,DNAString-method", "modifyNucleotides,DNAStringSet-method", "modifyNucleotides,ModString-method", "modifyNucleotides,ModStringSet-method", "modifyNucleotides,RNAString-method", "modifyNucleotides,RNAStringSet-method" ] }, { "page": "ModRNAString", "title": "ModDNAString class", "topics": [ "ModRNAString" ] }, { "page": "ModString", "title": "ModString objects", "topics": [ "==,ModString,ModString-method", "==,ModString,XString-method", "==,XString,ModString-method", "as.character,ModString-method", "as.vector,ModString-method", "ModDNAString-class", "ModRNAString-class", "ModString", "ModString,AsIs-method", "ModString,character-method", "ModString,factor-method", "ModString,MaskedModString-method", "ModString,ModString-method", "ModString,XString-method" ] }, { "page": "Modstrings", "title": "Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides.", "topics": [ "Modstrings" ] }, { "page": "Modstrings-internals", "title": "Modstrings internals", "topics": [ "modsDNA", "modsRNA", "Modstrings-internals", "MOD_RNA_DICT_MODOMICS", "MOD_RNA_DICT_TRNADB", "seqtype,ModDNAString-method", "seqtype,ModRNAString-method", "seqtype<-,ModString-method", "seqtype<-,ModStringSet-method", "XString,ModString-method", "XStringSet,ModStringSet-method" ] }, { "page": "ModStringSet", "title": "ModStringSet objects", "topics": [ "==,ModStringSet,ModStringSet-method", "==,ModStringSet,XStringSet-method", "==,XStringSet,ModStringSet-method", "as.character,ModStringSet-method", "ModDNAStringSet", "ModDNAStringSet-class", "ModRNAStringSet", "ModRNAStringSet-class", "ModStringSet", "ModStringSet,ANY-method", "ModStringSet,AsIs-method", "ModStringSet,character-method", "ModStringSet,factor-method", "ModStringSet,list-method", "ModStringSet,missing-method", "ModStringSet,ModString-method", "ModStringSet,ModStringSet-method", "show,ModStringSet-method" ] }, { "page": "ModStringSet-io", "title": "Read/write an ModStringSet object from/to a file", "topics": [ "ModStringSet-io", "readModDNAStringSet", "readModRNAStringSet", "writeModStringSet" ] }, { "page": "ModStringSetList", "title": "ModStringSetList", "topics": [ "ModDNAStringSetList", "ModDNAStringSetList-class", "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 specified locations containing nucleotide modifications", "topics": [ "replaceLetterAt", "replaceLetterAt,ModString-method", "replaceLetterAt,ModStringSet-method" ] }, { "page": "sanitizeInput", "title": "Sanitize input strings for use with ModString classes", "topics": [ "sanitizeFromModomics", "sanitizeFromtRNAdb", "sanitizeInput" ] }, { "page": "separate", "title": "Separating and combining a modification information into/from a 'XString' and a 'GRanges' object", "topics": [ "combineIntoModstrings", "combineIntoModstrings,XString,GRanges-method", "combineIntoModstrings,XStringSet,GRanges-method", "combineIntoModstrings,XStringSet,GRangesList-method", "combineModifications", "combineModifications,GRanges-method", "combineModifications,GRangesList-method", "incompatibleModifications", "incompatibleModifications,GRanges,XString-method", "incompatibleModifications,GRanges,XStringSet-method", "incompatibleModifications,GRangesList,XStringSet-method", "removeIncompatibleModifications", "removeIncompatibleModifications,GRanges,XString-method", "removeIncompatibleModifications,GRanges,XStringSet-method", "removeIncompatibleModifications,GRangesList,XStringSet-method", "separate", "separate,GRanges-method", "separate,GRangesList-method", "separate,ModString-method", "separate,ModStringSet-method" ] }, { "page": "alphabet", "title": "Base information for sequence characters of nucleotide strings containing modifications", "topics": [ "alphabet", "alphabet,ModString-method", "alphabet,ModStringSet-method", "fullName", "fullName,ModString-method", "fullName,ModStringSet-method", "nomenclature", "nomenclature,ModString-method", "nomenclature,ModStringSet-method", "shortName", "shortName,ModString-method", "shortName,ModStringSet-method" ] } ], "_readme": "https://github.com/bioc/Modstrings/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "Biostrings", "cli", "crayon", "generics", "GenomicRanges", "glue", "IRanges", "lifecycle", "magrittr", "rlang", "S4Vectors", "Seqinfo", "stringi", "stringr", "vctrs", "XVector" ], "_vignettes": [ { "source": "Modstrings.Rmd", "filename": "Modstrings.html", "title": "Modstrings", "author": "Felix G.M. Ernst & Denis L.J. Lafontaine", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Creating a ModRNAString object", "Streamlining object creation and modification", "Comparing ModString objects", "Conversion of ModString objects", "Quality scaled ModString", "Saving and reading ModString objects to/from file", "Pattern matching", "Future development", "Import example", "Sessioninfo", "References" ], "created": "2019-01-02 15:38:28", "modified": "2020-04-10 12:19:13", "commits": 12 }, { "source": "ModDNAString-alphabet.Rmd", "filename": "ModDNAString-alphabet.html", "title": "ModDNAString alphabet", "author": "Felix G.M. Ernst & Denis L.J. Lafontaine", "engine": "knitr::rmarkdown", "headings": [ "References" ], "created": "2019-01-02 15:38:28", "modified": "2020-02-01 14:21:56", "commits": 6 }, { "source": "ModRNAString-alphabet.Rmd", "filename": "ModRNAString-alphabet.html", "title": "ModRNAString alphabet", "author": "Felix G.M. Ernst & Denis L.J. Lafontaine", "engine": "knitr::rmarkdown", "headings": [ "References" ], "created": "2019-01-02 15:38:28", "modified": "2020-02-01 14:21:56", "commits": 6 } ], "_score": 7.033423755486949, "_indexed": true, "_nocasepkg": "modstrings", "_universes": [ "bioc", "felixernst" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T09:20:19.000Z", "distro": "noble", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "4227359bd34cd697b43c7e70138f7ba622cdf00c9093830d07cca3edf17a1a33", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" }, { "r": "4.6.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T09:21:03.000Z", "distro": "noble", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "aa8497273bfda58c0b8d6da660d8a771691ae1a1e9c87ec061c121c6f84f63d8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-05-30T12:45:41.000Z", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "e8adbfb5bdeeb4052c1b00f96ba19f326dfa61f0153fe93e2ef91eb9ca53eafc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" }, { "r": "4.6.0", "os": "mac", "version": "1.29.0", "date": "2026-05-30T12:45:44.000Z", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "d7950610e133e45671166c33ad74118eb0d34e08a1fc2fc3bbe4032c00dcbe65", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-05-30T09:20:04.000Z", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "28c5553df847a839ba91a06f25a7dfe2d1f44b3f85a24fccd939322467274d60", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-05-30T09:19:25.000Z", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "ba362674b6068eabbb0f1a9891a7b13d7c0e573b80dbb57c99e85d5895610eee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-05-30T09:19:07.000Z", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "525951beebaac0d43139dc011d15c9894f1b70dca75b4869a9eccf3bf89bd372", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" }, { "r": "4.6.0", "os": "win", "version": "1.29.0", "date": "2026-05-30T09:18:53.000Z", "commit": "4509228b0af0b505d0a14a5f87fa28996a89f553", "fileid": "0f45f541aa0c6d402dfa69f2501bd070e84303e1e5785ccaa7ed223b4f227e87", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675799399" } ] }