{ "_id": "6acdadd6a14063b82c3ac57e", "Package": "sesameData", "Type": "Package", "Title": "Supporting Data for SeSAMe Package", "Description": "Provides supporting annotation and test data for SeSAMe\npackage. This includes chip tango addresses, mapping\ninformation, performance annotation, and trained predictor for\nInfinium array data. This package provides user access to\nessential annotation data for working with many generations of\nthe Infinium DNA methylation array. Currently we support human\narray (HM27, HM450, EPIC), mouse array (MM285) and the\nHorvathMethylChip40 (Mammal40) array.", "Version": "1.31.1", "Authors@R": "c(person(\"Wanding\", \"Zhou\", role = c(\"aut\",\"cre\",\"fnd\"),\nemail = \"zhouwanding@gmail.com\", comment = c(ORCID = \"0000-0001-9126-1932\")),\nperson(\"Hui\", \"Shen\", role = c(\"aut\",\"fnd\"),\nemail = \"Hui.Shen@vai.org\"),\nperson(\"Timothy\", \"Triche\", role = \"ctb\"))", "License": "Artistic-2.0", "biocViews": "ExperimentData, MicroarrayData, Genome, ExperimentHub,\nMethylationArrayData", "URL": "https://github.com/zwdzwd/sesame", "BugReports": "https://github.com/zwdzwd/sesame/issues", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev libx11-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-10-12 02:43:00 UTC", "RemoteUrl": "https://github.com/bioc/sesameData", "RemoteRef": "HEAD", "RemoteSha": "7038450a5807a7e717542c904c7071edf1a9df3d", "Packaged": { "Date": "2026-10-13 03:54:40 UTC", "User": "root" }, "Author": "Wanding Zhou [aut, cre, fnd] (ORCID:\n),\nHui Shen [aut, fnd],\nTimothy Triche [ctb]", "Maintainer": "Wanding Zhou ", "_user": "bioc", "_type": "src", "_file": "sesameData_1.31.1.tar.gz", "_fileid": "https://r2.ropensci.org/5fd46fde0e6ff2b2c2b1f129246d19523e998bb7b64537c7e640824b2b7ccaee", "_filesize": 1677026, "_sha256": "5fd46fde0e6ff2b2c2b1f129246d19523e998bb7b64537c7e640824b2b7ccaee", "_expires": "2027-01-21T04:04:36.000Z", "_created": "2026-10-13T03:54:40.000Z", "_published": "2026-10-13T04:04:38.277Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38343277270", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 2 }, "_upstream": "https://github.com/bioc/sesameData", "_commit": { "id": "7038450a5807a7e717542c904c7071edf1a9df3d", "author": "Wanding Zhou ", "committer": "Wanding Zhou ", "message": "1.31.1: masks and probe addresses from InfiniumAnnotation v8.3 (Zenodo)\n\nEight objects, hosted on Zenodo record 23263026 (10.5281/zenodo.23263026),\nEHIDs requested:\n\n- HM450.address, EPIC.address, EPICv2.address, MSA.address: rebuilt from\n the InfiniumAnnotation v8.3 orderings (controls as ctl_
_\n rows, $controls NULL, $hg38 carried over). Replace EH7317, EH7323, EH8078\n and EH10271.\n- KYCG.{HM450,EPIC,EPICv2,MSA}.Mask.20261008: the M_* mask tracks of the\n InfiniumAnnotation .cm. They supersede KYCG.HM450.Mask.20240513,\n KYCG.EPIC.Mask.20220123, KYCG.EPICv2.Mask.20230314 and\n KYCG.MSA.Mask.20260122, now IN_USE FALSE.\n\nWith these and sesame >= 1.31.6, R's default QCDPB betas equal SeSAMe2's to\n~1e-15 on all four arrays (zhou-lab/sesame#1).\n\nR/sysdata.rda changes only those rows; the other 111 are identical.\n\nFix: the Zenodo fallback used before an EHID is assigned read every object\nwith load(), so an Rds object failed; it now uses readRDS for DispatchClass\nRds.\n", "time": 1791772980 }, "_maintainer": { "name": "Wanding Zhou", "email": "zhouwanding@gmail.com", "login": "zwdzwd", "description": "Working on Computational Epigenetics at CHOP and UPenn", "uuid": 7670339, "orcid": "0000-0001-9126-1932" }, "_distro": "resolute", "_jobs": [ { "job": 115120969991, "time": 166, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11788156831" }, { "job": 115120970053, "time": 327, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11788137242" }, { "job": 115120970009, "time": 547, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11788432105" }, { "job": 115118888193, "time": 513, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11788535492" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "ExperimentHub", "role": "Depends" }, { "package": "AnnotationHub", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.61.1", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "sesame", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2025-45", "n": 2 }, { "week": "2025-46", "n": 2 }, { "week": "2025-47", "n": 4 }, { "week": "2026-02", "n": 1 }, { "week": "2026-04", "n": 1 }, { "week": "2026-06", "n": 1 }, { "week": "2026-18", "n": 2 }, { "week": "2026-42", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "experimentdata", "microarraydata", "genome", "experimenthub", "methylationarraydata", "bioinformatics", "dna-methylation", "microarray", "datapkg" ], "_stars": 84, "_contributors": [ { "user": "zwdzwd", "count": 641, "uuid": 7670339 }, { "user": "ethanmoyer", "count": 37, "uuid": 57536747 }, { "user": "elaineficarra", "count": 24, "uuid": 80645344 }, { "user": "ttriche", "count": 20, "uuid": 4386 }, { "user": "dingwb", "count": 16, "uuid": 25999997 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "vjcitn", "count": 8, "uuid": 4624066 }, { "user": "golddc", "count": 2, "uuid": 90043071 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "henrikbengtsson", "count": 1, "uuid": 1616850 }, { "user": "hpages", "count": 1, "uuid": 8810451 }, { "user": "karltk", "count": 1, "uuid": 1164594 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_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/zwdzwd/sesame", "_searchresults": 157, "_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/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/sesameData.html" ], "_cranurl": false, "_exports": [ "inferPlatformFromProbeIDs", "sesameData_annoProbes", "sesameData_check_genome", "sesameData_check_platform", "sesameData_getGenomeInfo", "sesameData_getManifestGRanges", "sesameData_getProbesByGene", "sesameData_getProbesByRegion", "sesameData_getTxnGRanges", "sesameData_txnToGeneGRanges", "sesameDataCache", "sesameDataCacheAll", "sesameDataGet", "sesameDataGet_resetEnv", "sesameDataHas", "sesameDataList" ], "_help": [ { "page": "build_GENCODE_gtf", "title": "build GENCODE gtf", "topics": [ "build_GENCODE_gtf" ] }, { "page": "df_master", "title": "Master data frame for all object to cache", "topics": [ "df_master" ] }, { "page": "extend", "title": "Extend a GRanges", "topics": [ "extend" ] }, { "page": "inferPlatformFromProbeIDs", "title": "infer platform from Probe_IDs", "topics": [ "inferPlatformFromProbeIDs" ] }, { "page": "sesameData_annoProbes", "title": "Annotate Probes by Probe ID", "topics": [ "sesameData_annoProbes" ] }, { "page": "sesameData_check_genome", "title": "Find genome assembly version(s) supported for a platform", "topics": [ "sesameData_check_genome" ] }, { "page": "sesameData_check_platform", "title": "Check platform code", "topics": [ "sesameData_check_platform" ] }, { "page": "sesameData_getGenomeInfo", "title": "Get genome info files", "topics": [ "sesameData_getGenomeInfo" ] }, { "page": "sesameData_getManifestGRanges", "title": "get Infinium manifest GRanges", "topics": [ "sesameData_getManifestGRanges" ] }, { "page": "sesameData_getProbesByGene", "title": "Get Probes by Genes or Gene Promoters", "topics": [ "sesameData_getProbesByGene" ] }, { "page": "sesameData_getProbesByRegion", "title": "Get probes by genomic region", "topics": [ "sesameData_getProbesByRegion" ] }, { "page": "sesameData_getTxnGRanges", "title": "convert GRangesList to transcript GRanges", "topics": [ "sesameData_getTxnGRanges" ] }, { "page": "sesameData_txnToGeneGRanges", "title": "convert transcript GRanges to gene GRanges", "topics": [ "sesameData_txnToGeneGRanges" ] }, { "page": "sesameDataCache", "title": "Cache SeSAMe data", "topics": [ "sesameDataCache" ] }, { "page": "sesameDataCacheAll", "title": "Cache all SeSAMe data", "topics": [ "sesameDataCacheAll" ] }, { "page": "sesameDataGet", "title": "Get SeSAMe data", "topics": [ "sesameDataGet" ] }, { "page": "sesameDataGet_checkEnv", "title": "Check whether the title exists in cacheEnv", "topics": [ "sesameDataGet_checkEnv" ] }, { "page": "sesameDataGet_resetEnv", "title": "Empty cache environment to free memory", "topics": [ "sesameDataGet_resetEnv" ] }, { "page": "sesameDataHas", "title": "Whether sesameData has", "topics": [ "sesameDataHas" ] }, { "page": "sesameDataList", "title": "List all SeSAMe data", "topics": [ "sesameDataList" ] } ], "_readme": "https://github.com/bioc/sesameData/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "AnnotationHub", "askpass", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "clipr", "cpp11", "crayon", "curl", "DBI", "dbplyr", "dplyr", "ExperimentHub", "fastmap", "filelock", "generics", "GenomicRanges", "glue", "hms", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "readr", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr", "XVector", "yaml" ], "_vignettes": [ { "source": "sesameData.Rmd", "filename": "sesameData.html", "title": "SeSAMe Data User Guide", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Exported functions overview", "Genome Information", "Probes", "Manifest", "Raw Data Retrieval" ], "created": "2018-05-29 01:39:13", "modified": "2026-01-07 02:50:16", "commits": 27 } ], "_score": 9.966516050600921, "_indexed": true, "_nocasepkg": "sesamedata", "_universes": [ "bioc", "zwdzwd" ], "_previous": "1.31.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.1", "date": "2026-10-13T03:59:02.000Z", "distro": "resolute", "commit": "7038450a5807a7e717542c904c7071edf1a9df3d", "fileid": "https://r2.ropensci.org/8315e52d0e18483274fb64d6d6ba16398e127f82e24ad190ad6e6b530cb444bd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38343277270" }, { "r": "4.6.1", "os": "linux", "version": "1.31.1", "date": "2026-10-13T04:00:30.000Z", "distro": "resolute", "commit": "7038450a5807a7e717542c904c7071edf1a9df3d", "fileid": "https://r2.ropensci.org/5e316de62e1d7271d34088d4fb76f2e4d609dd49017c9b0c54130a1546d0cc73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38343277270" } ] }