{ "_id": "6a1ac11c1d7bb097a09d79bb", "Package": "normalize450K", "Type": "Package", "Title": "Preprocessing of Illumina Infinium 450K data", "Version": "1.41.0", "Date": "2016-11-29", "Author": "Jonathan Alexander Heiss", "Maintainer": "Jonathan Alexander Heiss ", "Description": "Precise measurements are important for epigenome-wide\nstudies investigating DNA methylation in whole blood samples,\nwhere effect sizes are expected to be small in magnitude. The\n450K platform is often affected by batch effects and proper\npreprocessing is recommended. This package provides functions\nto read and normalize 450K '.idat' files. The normalization\ncorrects for dye bias and biases related to signal intensity\nand methylation of probes using local regression. No adjustment\nfor probe type bias is performed to avoid the trade-off of\nprecision for accuracy of beta-values.", "License": "BSD_2_clause + file LICENSE", "biocViews": "Normalization, DNAMethylation, Microarray, TwoChannel,\nPreprocessing, MethylationArray", "NeedsCompilation": "no", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:42:18 UTC", "RemoteUrl": "https://github.com/bioc/normalize450K", "RemoteRef": "HEAD", "RemoteSha": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "Packaged": { "Date": "2026-05-30 07:22:59 UTC", "User": "root" }, "MD5sum": "f2d9ba281f79801b49627e22a729060a", "_user": "bioc", "_type": "src", "_file": "normalize450K_1.41.0.tar.gz", "_fileid": "cb9f55fecbe8577a731f679ec3a2dd36917cbb5e6ab207992357ddd78c5e799a", "_filesize": 3276438, "_sha256": "cb9f55fecbe8577a731f679ec3a2dd36917cbb5e6ab207992357ddd78c5e799a", "_created": "2026-05-30T07:22:59.000Z", "_published": "2026-05-30T10:51:08.719Z", "_jobs": [ { "job": 78633235968, "time": 151, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306450520" }, { "job": 78633235957, "time": 157, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306451265" }, { "job": 78633235954, "time": 189, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306455038" }, { "job": 78633235951, "time": 84, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307560513" }, { "job": 78633235969, "time": 125, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307565801" }, { "job": 78633058491, "time": 198, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306433716" }, { "job": 78633235949, "time": 101, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306444776" }, { "job": 78633235965, "time": 74, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306441844" }, { "job": 78633235980, "time": 83, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306442773" }, { "job": 78633235985, "time": 76, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306442165" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/normalize450K", "_commit": { "id": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380138 }, "_maintainer": { "name": "Jonathan Alexander Heiss", "email": "jonathan.heiss@posteo.de" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "illuminaio", "role": "Depends" }, { "package": "quadprog", "role": "Depends" }, { "package": "utils", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "normalization", "dnamethylation", "microarray", "twochannel", "preprocessing", "methylationarray" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 398, "source": "https://www.bioconductor.org/packages/stats/bioc/normalize450K" }, "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/normalize450K.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "dont_normalize450K", "estimateLC", "normalize450K", "read450K" ], "_help": [ { "page": "estimateLC", "title": "Estimation of Leukocyte composition for whole blood samples", "topics": [ "estimateLC" ] }, { "page": "read_and_normalize450K", "title": "Normalization of 450K data by LOESS method", "topics": [ "dont_normalize450K", "normalize450K", "read450K" ] } ], "_rundeps": [ "askpass", "base64", "Biobase", "BiocGenerics", "generics", "illuminaio", "openssl", "quadprog", "sys" ], "_vignettes": [ { "source": "read_and_normalize450K.Rnw", "filename": "read_and_normalize450K.pdf", "title": "Normalization of 450K data", "engine": "utils::Sweave", "headings": [], "created": "2015-12-01 22:52:06", "modified": "2016-04-01 09:19:21", "commits": 3 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "normalize450k", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T07:25:35.000Z", "distro": "noble", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "5a3fa94562dcef42e720e28cf73cbb2c5e84fdd76744466311654404b637f2a6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" }, { "r": "4.6.0", "os": "linux", "version": "1.41.0", "date": "2026-05-30T07:26:05.000Z", "distro": "noble", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "bbac6366fa5c8948932d95ad0a4ea01057f2abfb8c8e4c5c77519b769e94bc8f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" }, { "r": "4.5.3", "os": "mac", "version": "1.41.0", "date": "2026-05-30T10:36:35.000Z", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "546d5f1e1a9a94fa98798c5ae2a7fc174d613256e275281f9424120a9f163f8f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" }, { "r": "4.6.0", "os": "mac", "version": "1.41.0", "date": "2026-05-30T10:37:16.000Z", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "9812c6eb284cd72142d49f2f5d7a2a42ed9e11d41d0b36bc26c9864be6b3dcad", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" }, { "r": "4.6.0", "os": "wasm", "version": "1.41.0", "date": "2026-05-30T07:25:00.000Z", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "a661e1cf35f6273032b4a1fb1fcd8208f0f29687e6de3de16edc322f613d0556", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" }, { "r": "4.7.0", "os": "win", "version": "1.41.0", "date": "2026-05-30T07:24:14.000Z", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "b5d5ee37d62c4bbc1a123694e898093518b72216966526c090cba2c98938c9e5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" }, { "r": "4.5.3", "os": "win", "version": "1.41.0", "date": "2026-05-30T07:24:18.000Z", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "73a8ad577a862af5b470539b8f2e4cf8856229f58eb3b5c903dc9209e6b21d00", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" }, { "r": "4.6.0", "os": "win", "version": "1.41.0", "date": "2026-05-30T07:24:14.000Z", "commit": "b3b514ac52a07a43eed5a8fc0ef520ef98e89962", "fileid": "2607029882fa0f2742462b65e00c425404b597acaefdb9291d6e0429990e576e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677903476" } ] }