{ "_id": "6a1ad5201d7bb097a09e4cda", "Package": "EpiTxDb", "Type": "Package", "Title": "Storing and accessing epitranscriptomic information using the\nAnnotationDbi interface", "Version": "1.25.0", "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": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:06 UTC", "RemoteUrl": "https://github.com/bioc/EpiTxDb", "RemoteRef": "HEAD", "RemoteSha": "1bf0e241196de00db2bfbf9728d095277359caaf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:42:04 UTC", "User": "root" }, "Author": "Felix G.M. Ernst [aut, cre] (ORCID:\n)", "Maintainer": "Felix G.M. Ernst ", "MD5sum": "ab0fa08ab937c19acc3a231c0b0b9eec", "_user": "bioc", "_type": "src", "_file": "EpiTxDb_1.25.0.tar.gz", "_fileid": "928e232357d6db3cc7020edd7344bd2e613cdc958129ca2842c2205cc886e4b5", "_filesize": 330328, "_sha256": "928e232357d6db3cc7020edd7344bd2e613cdc958129ca2842c2205cc886e4b5", "_created": "2026-05-30T08:42:04.000Z", "_published": "2026-05-30T12:16:32.137Z", "_jobs": [ { "job": 78637307120, "time": 352, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306945066" }, { "job": 78637307149, "time": 573, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306967248" }, { "job": 78637307127, "time": 557, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306965430" }, { "job": 78637307135, "time": 313, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308098724" }, { "job": 78637307128, "time": 285, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308096301" }, { "job": 78636811912, "time": 605, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306911441" }, { "job": 78637307122, "time": 268, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306936838" }, { "job": 78637307154, "time": 443, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306954063" }, { "job": 78637307157, "time": 407, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306950487" }, { "job": 78637307159, "time": 439, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306953686" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/EpiTxDb", "_commit": { "id": "1bf0e241196de00db2bfbf9728d095277359caaf", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380726 }, "_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": "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": true, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 3 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_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", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 404, "source": "https://www.bioconductor.org/packages/stats/bioc/EpiTxDb" }, "_devurl": "https://github.com/felixernst/epitxdb", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EpiTxDb.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "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", "rappdirs", "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": 4.954242509439325, "_indexed": true, "_nocasepkg": "epitxdb", "_universes": [ "bioc", "felixernst" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T08:48:34.000Z", "distro": "noble", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "7b00c1395168cffb459b9cc0bdb8268ca3f4f52e8ce2a2954d4088cf8460bdd0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T08:48:08.000Z", "distro": "noble", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "defcb1e1a64277dab2166da737e32843f2b0883a2daf944b75451092899ef296", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-30T12:13:31.000Z", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "5fd66fe94262d7d67b935832a3d401993ab9c761efea84256bf1b0155be3ccf3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-30T12:13:20.000Z", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "d70de819247aac959554878e6d675bf9bc126051ad9f41186427caa5f038cecf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-30T08:47:21.000Z", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "f1de53f74ab14b6f9bd4685a437df9049bb85ec21eeb68043dfd9fdae0fca70b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T08:46:20.000Z", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "18ef3950dd031ccd84ee0d527203624e6b2e954224f4ddc13f0715d502ff44d2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-30T08:46:03.000Z", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "f216205690db27f6f476cf69eff1a661bee0f63d82b684082080498c1a95ca45", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T08:46:29.000Z", "commit": "1bf0e241196de00db2bfbf9728d095277359caaf", "fileid": "5f9940b351832ae684d416eb64f80fbccf9106c7f0af4671b67b42cbc3e03bc7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679323011" } ] }