{ "_id": "6ace3ba9a14063b82c3b1a80", "Package": "methylumi", "Type": "Package", "Title": "Handle Illumina methylation data", "Version": "2.59.3", "Date": "2026-08-14", "Author": "Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla", "biocViews": "DNAMethylation, TwoChannel, Preprocessing, QualityControl,\nCpGIsland", "Maintainer": "Sean Davis ", "Description": "This package provides classes for holding and manipulating\nIllumina methylation data. Based on eSet, it can contain MIAME\ninformation, sample information, feature information, and\nmultiple matrices of data. An \"intelligent\" import function,\nmethylumiR can read the Illumina text files and create a\nMethyLumiSet. methylumIDAT can directly read raw IDAT files\nfrom HumanMethylation27 and HumanMethylation450 microarrays.\nNormalization, background correction, and quality control\nfeatures for GoldenGate, Infinium, and Infinium HD arrays are\nalso included.", "Collate": "AllGenerics.R MethyLumiSet-class.R MethyLumiM-class.R\nMoreGenerics.R Methods.R bgcorr.R coercions.R data.R\ndetectionpval.R featureFilter.R mclapply_replace.R\nmethylData-class.R methylumIDAT.R methylumiCSV.R methylumiR.R\nnormalization.R plotNegOob.R qc.probe.plot.R readIDAT2.R\nstripMethyLumiSet.R utilities.R varFilter.R", "VignetteBuilder": "quarto", "URL": "https://seandavi.github.io/methylumi/,\nhttps://github.com/seandavi/methylumi", "BugReports": "https://github.com/seandavi/methylumi/issues", "License": "GPL-2", "Encoding": "UTF-8", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-08-14 16:33:14 UTC", "RemoteUrl": "https://github.com/bioc/methylumi", "RemoteRef": "HEAD", "RemoteSha": "4232eaf043694b8b8e2bfe1095f03185be39a8af", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-13 13:31:33 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "methylumi_2.59.3.tar.gz", "_fileid": "https://r2.ropensci.org/b654cbe801d302f930fe3cca282553da15ab44281fb3e516a0e4bb55de54c360", "_filesize": 6740553, "_sha256": "b654cbe801d302f930fe3cca282553da15ab44281fb3e516a0e4bb55de54c360", "_expires": "2027-01-21T14:09:41.000Z", "_created": "2026-10-13T13:31:33.000Z", "_published": "2026-10-13T14:09:45.791Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38404543783", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 2, "warning": 5, "note": 14 }, "_upstream": "https://github.com/bioc/methylumi", "_commit": { "id": "4232eaf043694b8b8e2bfe1095f03185be39a8af", "author": "Sean Davis ", "committer": "GitHub ", "message": "Install methylumi into the real library before building the pkgdown site (#52)\n\npkgdown::build_site(install = TRUE) installs the package into a temporary\nlibrary that exists only on the calling R process's .libPaths(). The articles\nare .qmd, so pkgdown renders them by shelling out to the Quarto CLI, which\nstarts a fresh R session per file -- and that session inherits none of the\ntemporary library. library(methylumi) in the vignettes therefore resolved\nagainst the stale methylumi already in the container's site-library, and the\nbuild died with the long-fixed defunct import from #28:\n\n ! package or namespace load failed for 'methylumi':\n object 'parallel' is not exported by 'namespace:lattice'\n Quitting from methylumi.qmd:83-93 [load]\n\nbuild_site() renders articles with quiet = TRUE, which is why the log showed\nonly 'Error returned by quarto CLI'.\n\nInstall into site-library ourselves and pass install = FALSE, so the child\nQuarto sessions see the package being documented.\n\nCo-authored-by: Claude Opus 5 ", "time": 1786725194 }, "_maintainer": { "name": "Sean Davis", "email": "seandavi@gmail.com", "login": "seandavi", "description": "Software developer, Pediatric oncologist, Cancer 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Illumina Methylation data", "topics": [ "methylated,MethyLumi-method", "methylated<-,MethyLumi,matrix-method", "MethyLumi-class", "pvals,MethyLumi-method", "pvals<-,MethyLumi,matrix-method", "qcplot,Methylumi-method", "summary,MethyLumi-method", "unmethylated,MethyLumi-method", "unmethylated<-,MethyLumi,matrix-method" ] }, { "page": "MethyLumi-strippers", "title": "Strip excessive probe-level data from MethyLumiSets", "topics": [ "MethyLumi-strippers", "stripBeadNs", "stripBeadSDs", "stripMethyLumiSet", "stripOOB" ] }, { "page": "methylumIDAT", "title": "methylumIDAT", "topics": [ "methylumIDAT" ] }, { "page": "methylumiGenerics", "title": "Generics defined in methylumi", "topics": [ "betas,GenomicMethylSet-method", "betas,MethylSet-method", "betas,RangedSummarizedExperiment-method", "combine27k450k", "controlData", "controlData<-", "cy3", "Cy3.N", "Cy3<-", "cy5", "Cy5.N", "Cy5<-", "dataType", "dataType<-", "designIItoMandU", "designItoMandU", "detection", "detection<-", "diagnostics", 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