{ "_id": "6ae7aefe818c9e3ef6dbcbc2", "Package": "EpiTxDb", "Type": "Package", "Title": "Storing and accessing epitranscriptomic information using the\nAnnotationDbi interface", "Version": "1.24.0", "Date": "2025-09-23", "Authors@R": "person(\"Felix G.M.\", \n\"Ernst\",\nemail = \"felix.gm.ernst@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5064-0928\"))", "Description": "EpiTxDb facilitates the storage of epitranscriptomic\ninformation. More specifically, it can keep track of\nmodification identity, position, the enzyme for introducing it\non the RNA, a specifier which determines the position on the\nRNA to be modified and the literature references each\nmodification is associated with.", "License": "Artistic-2.0", "Encoding": "UTF-8", "LazyData": "false", "biocViews": "Software, Epitranscriptomics", "Collate": "'AllGenerics.R' 'EpiTxDb-SELECT-helpers.R' 'EpiTxDb-schema.R'\n'EpiTxDb.R' 'EpiTxDb-class.R' 'makeEpiTxDb.R'\n'makeEpiTxDbFromGRanges.R' 'shiftGenomicToTranscript.R'\n'makeEpiTxDbFromRMBase.R' 'makeEpiTxDbFromtRNAdb.R'\n'modifications.R' 'modificationsBy.R' 'ranges-helpers.R'\n'select-methods.R'", "RoxygenNote": "7.3.3", "BugReports": "https://github.com/FelixErnst/EpiTxDb/issues", "URL": "https://github.com/FelixErnst/EpiTxDb", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:52:06 UTC", "RemoteUrl": "https://github.com/bioc/EpiTxDb", "RemoteRef": "RELEASE_3_23", "RemoteSha": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 18:12:12 UTC", "User": "root" }, "Author": "Felix G.M. Ernst [aut, cre] (ORCID:\n)", "Maintainer": "Felix G.M. Ernst ", "_user": "bioc-release", "_type": "src", "_file": "EpiTxDb_1.24.0.tar.gz", "_fileid": "https://r2.ropensci.org/448f4006d423b0c3013b4e26939a3b812a728176f29d0493d16fdc7508ea6ad8", "_filesize": 331390, "_sha256": "448f4006d423b0c3013b4e26939a3b812a728176f29d0493d16fdc7508ea6ad8", "_expires": "2027-02-09T21:28:28.000Z", "_created": "2026-11-01T18:12:12.000Z", "_published": "2026-11-01T21:28:30.516Z", "_upstream": "https://github.com/bioc/EpiTxDb", "_status": "success", "_maintainer": { "name": "Felix G.M. Ernst", "email": "felix.gm.ernst@outlook.com", "login": "felixernst", "description": "", "uuid": 17824332, "orcid": "0000-0001-5064-0928" }, "_jobs": [ { "job": 124934267726, "time": 372, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13095798399" }, { "job": 124934267636, "time": 596, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13096480511" }, { "job": 124934267615, "time": 588, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13095629616" }, { "job": 124934267651, "time": 277, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13101398802" }, { "job": 124934267711, "time": 530, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13101638191" }, { "job": 124927495487, "time": 554, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13094743470" }, { "job": 124934267627, "time": 272, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13095429991" }, { "job": 124934267688, "time": 478, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13094714992" }, { "job": 124934267710, "time": 479, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13095142655" }, { "job": 124934267646, "time": 467, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13094699955" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953", "_commit": { "id": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380726 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Depends" }, { "package": "Modstrings", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "curl", "role": "Imports" }, { "package": "rex", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "txdbmaker", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "tRNAdbImport", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "httptest", "role": "Suggests" }, { "package": "AnnotationHub", "role": "Suggests" }, { "package": "ensembldb", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "EpiTxDb.Hs.hg38", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "BSgenome.Scerevisiae.UCSC.sacCer3", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg38.knownGene", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "epitranscriptomics" ], "_stars": 0, "_contributors": [ { "user": "felixernst", "count": 109, "uuid": 17824332 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 525, "source": "https://www.bioconductor.org/packages/stats/bioc/EpiTxDb" }, "_devurl": "https://github.com/felixernst/epitxdb", "_searchresults": 11, "_abi": { "exports": [ { "key": "EpiTxDb::EpiTxDb", "hash": "8f02257c5294dbf7" }, { "key": "EpiTxDb::generic:modifications", "hash": "e2b673c0da1dcd26" }, { "key": "EpiTxDb::generic:modificationsBy", "hash": "41dd496e77a50b5b" }, { "key": "EpiTxDb::generic:modifiedSeqsByTranscript", "hash": "2bce214737b01013" }, { "key": "EpiTxDb::generic:positionSequence", "hash": "e54b3d52452b9b9d" }, { "key": "EpiTxDb::generic:rescale", "hash": "436c3f0a5bf74b09" }, { "key": "EpiTxDb::generic:shiftGenomicToTranscript", "hash": "a186ea3f09918cad" }, { "key": "EpiTxDb::generic:shiftTranscriptToGenomic", "hash": "a702e3c6b465d5a8" } ], "imports": [ { "key": "AnnotationDbi::AnnotationDb", "hash": "a4bdd04b3ae79fb2" }, { "key": "AnnotationDbi::generic:columns", "hash": "05e2c7067b5e829f" }, { "key": "AnnotationDbi::generic:keys", "hash": "931ea12e0913cf48" }, { "key": "AnnotationDbi::generic:keytypes", "hash": "1861f8e46f59b1c3" }, { "key": "AnnotationDbi::generic:select", "hash": "ba90536ae2ef92ed" }, { "key": "BiocGenerics::generic:organism", "hash": "ab8f0a44c2b4a1e8" }, { "key": "Seqinfo::generic:seqinfo", "hash": "1eb5bbe2fff73b75" }, { "key": "Seqinfo::generic:seqlevels", "hash": "89deec4b5b51a8a1" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EpiTxDb.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/felixernst/epitxdb", "_realowner": "bioc", "_cranurl": false, "_exports": [ "as.list", "columns", "downloadRMBaseFiles", "EPITXDB_RMBASE_URL", "getRMBaseDataAsGRanges", "gettRNAdbDataAsGRanges", "keys", "keytypes", "listAvailableGenomesFromRMBase", "listAvailableModFromRMBase", "listAvailableOrganismsFromRMBase", "listAvailableOrganismsFromtRNAdb", "makeEpiTxDb", "makeEpiTxDbFromGRanges", "makeEpiTxDbFromRMBase", "makeEpiTxDbFromRMBaseFiles", "makeEpiTxDbFromtRNAdb", "modifications", "modificationsBy", "modifiedSeqsByTranscript", "organism", "positionSequence", "rescale", "select", "seqinfo", "seqlevels", "shiftGenomicToTranscript", "shiftTranscriptToGenomic" ], "_datasets": [ { "name": "rmbase_data", "title": "EpiTxDb internal data", "object": "rmbase_data", "file": "rmbase_data.rda", "class": [ "data.frame" ], "fields": [ "species", "mod", "dataSet", "organism", "genome", "file" ], "rows": 38, "table": true, "tojson": true } ], "_help": [ { "page": "EpiTxDb-class", "title": "EpiTxDb objects", "topics": [ ".EpiTxDb", "as.list,EpiTxDb-method", "EpiTxDb", "EpiTxDb-class", "organism,EpiTxDb-method", "seqinfo,EpiTxDb-method", "seqlevels,EpiTxDb-method" ] }, { "page": "EpiTxDb-data", "title": "EpiTxDb internal data", "topics": [ "EpiTxDb-data", "rmbase_data" ] }, { "page": "EpiTxDb-package-hash-single-quote", "title": "'EpiTxDb' - Storing and accessing epitranscriptomic information using the AnnotationDbi interface", "topics": [ "EpiTxDb-package#'" ] }, { "page": "makeEpiTxDb", "title": "Creating a 'EpiTxDb' from user supplied annotations as 'data.frame's", "topics": [ "makeEpiTxDb" ] }, { "page": "makeEpiTxDbFromGRanges", "title": "Create a 'EpiTxDb' object from a 'GRanges' object", "topics": [ "makeEpiTxDbFromGRanges" ] }, { "page": "makeEpiTxDbFromRMBase", "title": "Create a 'EpiTxDb' object from RMBase v2.0 online resources", "topics": [ "downloadRMBaseFiles", "EPITXDB_RMBASE_URL", "getRMBaseDataAsGRanges", "listAvailableGenomesFromRMBase", "listAvailableModFromRMBase", "listAvailableOrganismsFromRMBase", "makeEpiTxDbFromRMBase", "makeEpiTxDbFromRMBaseFiles" ] }, { "page": "makeEpiTxDbFromtRNAdb", "title": "Create a 'EpiTxDb' object from tRNAdb resources", "topics": [ "gettRNAdbDataAsGRanges", "listAvailableOrganismsFromtRNAdb", "makeEpiTxDbFromtRNAdb" ] }, { "page": "modifications", "title": "Getting modification data from a 'EpiTxDb-object'", "topics": [ "modifications", "modifications,EpiTxDb-method", "modificationsBy", "modificationsBy,EpiTxDb-method", "modifiedSeqsByTranscript", "modifiedSeqsByTranscript,EpiTxDb,DNAStringSet-method" ] }, { "page": "positionSequence", "title": "Generate integer sequences from position information of 'Ranges'", "topics": [ "as.integer,Ranges-method", "positionSequence", "positionSequence,Ranges-method", "positionSequence,RangesList-method" ] }, { "page": "rescale", "title": "Rescaling 'Ranges' object", "topics": [ "rescale", "rescale,GRanges-method", "rescale,GRangesList-method", "rescale,IRanges-method", "rescale,IRangesList-method" ] }, { "page": "select", "title": "Using the \"select\" interface on 'EpiTxDb' objects", "topics": [ "columns", "columns,EpiTxDb-method", "keys", "keys,EpiTxDb-method", "keytypes", "keytypes,EpiTxDb-method", "select", "select,EpiTxDb-method" ] }, { "page": "shiftGenomicToTranscript", "title": "Shift 'GRanges' coordinates based on another 'GRanges' object", "topics": [ "shiftGenomicToTranscript", "shiftGenomicToTranscript,GRanges,GRangesList-method", "shiftGenomicToTranscript,GRangesList,GRangesList-method", "shiftTranscriptToGenomic", "shiftTranscriptToGenomic,GRanges,GRangesList-method", "shiftTranscriptToGenomic,GRangesList,GRangesList-method" ] } ], "_readme": "https://github.com/bioc/EpiTxDb/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "farver", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gtable", "hms", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "Modstrings", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "RCurl", "restfulr", "rex", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "Structstrings", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tRNA", "tRNAdbImport", "txdbmaker", "UCSC.utils", "utf8", "vctrs", "viridisLite", "withr", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "EpiTxDb.Rmd", "filename": "EpiTxDb.html", "title": "EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface", "author": "Felix G.M. Ernst", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Introduction", "Getting started", "Accessing RNA modifications", "Shifting coordinates from genomic to transcriptomic", "Session info", "References" ], "created": "2020-02-06 15:33:45", "modified": "2021-03-25 10:01:39", "commits": 10 }, { "source": "EpiTxDb-creation.Rmd", "filename": "EpiTxDb-creation.html", "title": "EpiTxDb: creating an EpiTxDb object", "author": "Felix G.M. Ernst", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "makeEpiTxDb and makeEpiTxDbFromGRanges", "makeEpiTxDbFromtRNAdb", "makeEpiTxDbFromRMBase", "Session info", "References" ], "created": "2020-02-26 13:45:49", "modified": "2024-03-24 00:48:14", "commits": 3 } ], "_score": 4.819543935541869, "_indexed": false, "_nocasepkg": "epitxdb", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/EpiTxDb", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.24.0", "date": "2026-11-01T18:41:14.000Z", "distro": "resolute", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/93622cc4317cbc1ab28a45e6b351a5bd84a87b81b2d8add0b838688648f62fe5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" }, { "r": "4.6.2", "os": "linux", "version": "1.24.0", "date": "2026-11-01T18:41:07.000Z", "distro": "resolute", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/5cc69277762a6d539c78cade80674a9857416c26b1ef0b659615c8c5a2d7c581", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" }, { "r": "4.5.3", "os": "mac", "version": "1.24.0", "date": "2026-11-01T21:21:21.000Z", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/bc9f82d7077a6423665e97236347b392fa19f8d40224d9e012da5b8744d8e02a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" }, { "r": "4.6.2", "os": "mac", "version": "1.24.0", "date": "2026-11-01T21:22:54.000Z", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/d4bcd1172b2423a8af5799d359905c90d7dd7ab9d4f72b294eaa77ea987ea430", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" }, { "r": "4.6.0", "os": "wasm", "version": "1.24.0", "date": "2026-11-01T18:39:43.000Z", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/b53c62025cc10159373c10d325b3f243280cd4b70aed567cbd354bac8904a18c", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" }, { "r": "4.7.0", "os": "win", "version": "1.24.0", "date": "2026-11-01T18:17:11.000Z", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/4942da877378bc1732bc18f15ef5dda65e2b02680c068593717e3bc28277e56f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" }, { "r": "4.5.3", "os": "win", "version": "1.24.0", "date": "2026-11-01T18:16:57.000Z", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/333ca2d3a57ed08f6f39181225708e175c93eee52ed6bfa6f9601e039f0f0b41", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" }, { "r": "4.6.2", "os": "win", "version": "1.24.0", "date": "2026-11-01T18:17:00.000Z", "commit": "cafb7bdd9cc60c0ad8895ef58223e69244932ee4", "fileid": "https://r2.ropensci.org/b554a5cb6300cbd54a8ddb986744f2f09fb7fcff0db119a186b32f2f87296504", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/41332145953" } ] }