{ "_id": "6aca188bfe5cc25786e84a43", "Package": "methylclockData", "Title": "Data for methylclock package", "Description": "Data resources used by the methylclock package to estimate\nchronological, gestational and biological age from DNA\nmethylation, and to adjust those estimates for blood cell\ncomposition. It provides the coefficient tables of the\nindividual clocks, the CpG sets of the mitotic counters, the\nweights of the neural network clock, and example methylation\ndatasets. It also provides nine cell type reference datasets\n(andrews and bakulski cord blood, blood gse35069, blood\ngse35069 chen, blood gse35069 complete, combined cord blood,\ncord blood gse68456, gervin and lyle cord blood, guintivano\ndlpfc, saliva gse48472), downloaded from meffil\n(https://github.com/perishky/meffil/), which are used to\nestimate cell counts for the extrinsic epigenetic age\nacceleration (EEAA) method. All resources are served through\nExperimentHub.", "Version": "1.21.4", "Authors@R": "c(person(\"Juan R.\", \"Gonzalez\", ,\"juanr.gonzalez@isglobal.org\", role = c(\"aut\")),\nperson(\"Dolors\", \"Pelegri-Siso\", ,\"dolors.pelegri@isglobal.org\", role = c(\"aut\", \"cre\")))", "BugReports": "https://github.com/isglobal-brge/methylclockData/issues", "URL": "https://github.com/isglobal-brge/methylclockData", "biocViews": "SpecimenSource, ExperimentHub, Tissue, OrganismData,\nHomo_sapiens_Data", "License": "MIT + file LICENSE", "NeedsCompilation": "no", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "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": "2026-09-09 06:12:52 UTC", "RemoteUrl": "https://github.com/bioc/methylclockData", "RemoteRef": "HEAD", "RemoteSha": "4787fc57de0ccf74b9e21bdb89c8d1e0eaba16df", "Packaged": { "Date": "2026-10-10 10:42:08 UTC", "User": "root" }, "Author": "Juan R. Gonzalez [aut],\nDolors Pelegri-Siso [aut, cre]", "Maintainer": "Dolors Pelegri-Siso ", "_user": "bioc", "_type": "src", "_file": "methylclockData_1.21.4.tar.gz", "_fileid": "https://r2.ropensci.org/81eddf51d2f7f348773ff01cd23d13400bcd16771043a36f24c049017355c259", "_filesize": 155604, "_sha256": "81eddf51d2f7f348773ff01cd23d13400bcd16771043a36f24c049017355c259", "_expires": "2027-01-18T10:50:50.000Z", "_created": "2026-10-10T10:42:08.000Z", "_published": "2026-10-10T10:50:51.902Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38045603684", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_upstream": "https://github.com/bioc/methylclockData", "_commit": { "id": "4787fc57de0ccf74b9e21bdb89c8d1e0eaba16df", "author": "dpelegri <43083225+dpelegri@users.noreply.github.com>", "committer": "dpelegri <43083225+dpelegri@users.noreply.github.com>", "message": " in the coefGarma ExperimentHub id EH10518 and bump to 1.21.4\n\nThe hubs team added the coefGarma resource to ExperimentHub devel on 2026-09-04 as EH10518 (49 methylclockData records in total). The get_coefGarma() accessor now retrieves that id and its example is runnable.\n", "time": 1788934372 }, "_maintainer": { "name": "Dolors Pelegri-Siso", "email": "dolors.pelegri@isglobal.org", "login": "isglobal-exposomehub", "description": "", "uuid": 79249071 }, "_distro": "resolute", "_jobs": [ { "job": 114195118753, "time": 152, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11667239361" }, { "job": 114195118755, "time": 472, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11667865050" }, { "job": 114195118733, "time": 398, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11666933814" }, { "job": 114194430276, "time": 240, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11667219025" } ], "_registered": true, "_dependencies": [ { "package": "ExperimentHubData", "role": "Imports" }, { "package": "ExperimentHub", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-32", "n": 5 }, { "week": "2026-34", "n": 1 }, { "week": "2026-35", "n": 1 }, { "week": "2026-37", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.4", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "specimensource", "experimenthub", "tissue", "organismdata", "homo_sapiens_data", "datapkg" ], "_stars": 0, "_contributors": [ { "user": "dpelegri", "count": 61, "uuid": 43083225 }, { "user": "hpages", "count": 10, "uuid": 8810451 }, { "user": "lshep", "count": 8, "uuid": 18724380 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "isglobal-brge", "count": 1, "uuid": 22591681 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/isglobal-brge/methylclockdata", "_searchresults": 19, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/methylclockData.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "get_coefAdaptAge", "get_coefAltumAge", "get_coefAltumAgeRef", "get_coefBLUP", "get_coefBohlin", "get_coefCausAge", "get_coefDamAge", "get_coefDunedinPACE", "get_coefDunedinPACEGS", "get_coefEN", "get_coefEPIC", "get_coefEpiTOC1", "get_coefEpiTOC2", "get_coefGarma", "get_coefHannum", "get_coefHorvath", "get_coefHypoClock", "get_coefKnightGA", "get_coefLeeGA", "get_coefLevine", "get_coefLin", "get_coefMayneGA", "get_coefMcCartneyAlcohol", "get_coefMcCartneyBMI", "get_coefMcCartneyBodyFat", "get_coefMcCartneyEducation", "get_coefMcCartneyHDL", "get_coefMcCartneyLDL", "get_coefMcCartneySmoking", "get_coefMcCartneyTotalChol", "get_coefMcCigarette", "get_coefNEOaPMA450K", "get_coefNEOaPMAEPIC", "get_coefNEOaPNA450K", "get_coefNEOaPNAEPIC", "get_coefPedBE", "get_coefRepliTali", "get_coefSkin", "get_coefStemTOC", "get_coefTL", "get_coefVidalBralo", "get_coefWeidner", "get_coefWu", "get_cpgs_bn", "get_MethylationDataExample", "get_probeAnnotation21kdatMethUsed", "get_references", "get_TestDataset" ], "_help": [ { "page": "get_coefAdaptAge", "title": "coefAdaptAge", "topics": [ "get_coefAdaptAge" ] }, { "page": "get_coefAltumAge", "title": "coefAltumAge", "topics": [ "get_coefAltumAge" ] }, { "page": "get_coefAltumAgeRef", "title": "coefAltumAgeRef", "topics": [ "get_coefAltumAgeRef" ] }, { "page": "get_coefBLUP", "title": "coefBLUP", "topics": [ "get_coefBLUP" ] }, { "page": "get_coefBohlin", "title": "coefBohlin", "topics": [ "get_coefBohlin" ] }, { "page": "get_coefCausAge", "title": "coefCausAge", "topics": [ "get_coefCausAge" ] }, { "page": "get_coefDamAge", "title": "coefDamAge", "topics": [ "get_coefDamAge" ] }, { "page": "get_coefDunedinPACE", "title": "coefDunedinPACE", "topics": [ "get_coefDunedinPACE" ] }, { "page": "get_coefDunedinPACEGS", "title": "coefDunedinPACEGS", "topics": [ "get_coefDunedinPACEGS" ] }, { "page": "get_coefEN", "title": "coefEN", "topics": [ "get_coefEN" ] }, { "page": "get_coefEPIC", "title": "coefEPIC", "topics": [ "get_coefEPIC" ] }, { "page": "get_coefEpiTOC1", "title": "coefEpiTOC1", "topics": [ "get_coefEpiTOC1" ] }, { "page": "get_coefEpiTOC2", "title": "coefEpiTOC2", "topics": [ "get_coefEpiTOC2" ] }, { "page": "get_coefGarma", "title": "coefGarma", "topics": [ "get_coefGarma" ] }, { "page": "get_coefHannum", "title": "coefHannum", "topics": [ "get_coefHannum" ] }, { "page": "get_coefHorvath", "title": "coefHorvath", "topics": [ "get_coefHorvath" ] }, { "page": "get_coefHypoClock", "title": "coefHypoClock", "topics": [ "get_coefHypoClock" ] }, { "page": "get_coefKnightGA", "title": "coefKnightGA", "topics": [ "get_coefKnightGA" ] }, { "page": "get_coefLeeGA", "title": "coefLeeGA", "topics": [ "get_coefLeeGA" ] }, { "page": "get_coefLevine", "title": "coefLevine", "topics": [ "get_coefLevine" ] }, { "page": "get_coefLin", "title": "coefLin", "topics": [ "get_coefLin" ] }, { "page": "get_coefMayneGA", "title": "coefMayneGA", "topics": [ "get_coefMayneGA" ] }, { "page": "get_coefMcCartneyAlcohol", "title": "coefMcCartneyAlcohol", "topics": [ "get_coefMcCartneyAlcohol" ] }, { "page": "get_coefMcCartneyBMI", "title": "coefMcCartneyBMI", "topics": [ "get_coefMcCartneyBMI" ] }, { "page": "get_coefMcCartneyBodyFat", "title": "coefMcCartneyBodyFat", "topics": [ "get_coefMcCartneyBodyFat" ] }, { "page": "get_coefMcCartneyEducation", "title": "coefMcCartneyEducation", "topics": [ "get_coefMcCartneyEducation" ] }, { "page": "get_coefMcCartneyHDL", "title": "coefMcCartneyHDL", "topics": [ "get_coefMcCartneyHDL" ] }, { "page": "get_coefMcCartneyLDL", "title": "coefMcCartneyLDL", "topics": [ "get_coefMcCartneyLDL" ] }, { "page": "get_coefMcCartneySmoking", "title": "coefMcCartneySmoking", "topics": [ "get_coefMcCartneySmoking" ] }, { "page": "get_coefMcCartneyTotalChol", "title": "coefMcCartneyTotalChol", "topics": [ "get_coefMcCartneyTotalChol" ] }, { "page": "get_coefMcCigarette", "title": "coefMcCigarette", "topics": [ "get_coefMcCigarette" ] }, { "page": "get_coefNEOaPMA450K", "title": "coefNEOaPMA450K", "topics": [ "get_coefNEOaPMA450K" ] }, { "page": "get_coefNEOaPMAEPIC", "title": "coefNEOaPMAEPIC", "topics": [ "get_coefNEOaPMAEPIC" ] }, { "page": "get_coefNEOaPNA450K", "title": "coefNEOaPNA450K", "topics": [ "get_coefNEOaPNA450K" ] }, { "page": "get_coefNEOaPNAEPIC", "title": "coefNEOaPNAEPIC", "topics": [ "get_coefNEOaPNAEPIC" ] }, { "page": "get_coefPedBE", "title": "coefPedBE", "topics": [ "get_coefPedBE" ] }, { "page": "get_coefRepliTali", "title": "coefRepliTali", "topics": [ "get_coefRepliTali" ] }, { "page": "get_coefSkin", "title": "coefSkin", "topics": [ "get_coefSkin" ] }, { "page": "get_coefStemTOC", "title": "coefStemTOC", "topics": [ "get_coefStemTOC" ] }, { "page": "get_coefTL", "title": "coefTL", "topics": [ "get_coefTL" ] }, { "page": "get_coefVidalBralo", "title": "coefVidalBralo", "topics": [ "get_coefVidalBralo" ] }, { "page": "get_coefWeidner", "title": "coefWeidner", "topics": [ "get_coefWeidner" ] }, { "page": "get_coefWu", "title": "Wu", "topics": [ "get_coefWu" ] }, { "page": "get_cpgs_bn", "title": "cpgs_bn", "topics": [ "get_cpgs_bn" ] }, { "page": "get_MethylationDataExample", "title": "MethylationDataExample55", "topics": [ "get_MethylationDataExample" ] }, { "page": "get_probeAnnotation21kdatMethUsed", "title": "probeAnnotation21kdatMethUsed", "topics": [ "get_probeAnnotation21kdatMethUsed" ] }, { "page": "get_references", "title": "references", "topics": [ "get_references" ] }, { "page": "get_TestDataset", "title": "TestDataset", "topics": [ "get_TestDataset" ] } ], "_readme": "https://github.com/bioc/methylclockData/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "AnnotationForge", "AnnotationHub", "AnnotationHubData", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocCheck", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "BiocVersion", "biocViews", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "callr", "cigarillo", "cli", "codetools", "commonmark", "cpp11", "crayon", "curl", "DBI", "dbplyr", "dplyr", "evaluate", "ExperimentHub", "ExperimentHubData", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "graph", "highr", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "knitr", "lambda.r", "lifecycle", "magrittr", "memoise", "mime", "openssl", "OrganismDbi", "otel", "pillar", "pkgconfig", "png", "processx", "ps", "purrr", "R6", "rappdirs", "RBGL", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "RUnit", "rvest", "S4Vectors", "selectr", "Seqinfo", "snow", "stringdist", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "UCSC.utils", "utf8", "vctrs", "withr", "xfun", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "methylcockData.Rmd", "filename": "methylcockData.html", "title": "references", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Chronological DNAm age (in years)", "Gestational DNAm age (in weeks)", "How to load data", "sessionInfo()" ], "created": "2020-11-18 07:57:58", "modified": "2022-03-07 20:23:16", "commits": 5 } ], "_score": 5.357934847000454, "_indexed": true, "_nocasepkg": "methylclockdata", "_universes": [ "bioc", "isglobal-exposomehub", "isglobal-brge" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.4", "date": "2026-10-10T10:45:37.000Z", "distro": "resolute", "commit": "4787fc57de0ccf74b9e21bdb89c8d1e0eaba16df", "fileid": "https://r2.ropensci.org/87cecaff447e6a2b01f70dee15764b169ad3f1f5bdc874f81c955030f23ef0b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38045603684" }, { "r": "4.6.1", "os": "linux", "version": "1.21.4", "date": "2026-10-10T10:45:32.000Z", "distro": "resolute", "commit": "4787fc57de0ccf74b9e21bdb89c8d1e0eaba16df", "fileid": "https://r2.ropensci.org/c683f17aa03d481b52bdd95f62a03e93c41b71ed6f048f2c0e8ed0d46706b5a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38045603684" } ] }