{ "_id": "6a1afd611d7bb097a09fdf01", "Package": "skewr", "Title": "Visualize Intensities Produced by Illumina's Human Methylation\n450k BeadChip", "Version": "1.45.0", "Authors@R": "c(person(\"Ryan\", \"Putney\", role = c(\"cre\", \"aut\"), email =\n\"ryanputney@gmail.com\"), person(\"Steven\", \"Eschrich\", role =\n\"aut\"), person(\"Anders\", \"Berglund\", role = \"aut\"))", "Description": "The skewr package is a tool for visualizing the output of\nthe Illumina Human Methylation 450k BeadChip to aid in quality\ncontrol. It creates a panel of nine plots. Six of the plots\nrepresent the density of either the methylated intensity or the\nunmethylated intensity given by one of three subsets of the\n485,577 total probes. These subsets include Type I-red, Type\nI-green, and Type II.The remaining three distributions give the\ndensity of the Beta-values for these same three subsets. Each\nof the nine plots optionally displays the distributions of the\n\"rs\" SNP probes and the probes associated with imprinted genes\nas series of 'tick' marks located above the x-axis.", "VignetteBuilder": "knitr", "License": "GPL-2", "biocViews": "DNAMethylation, TwoChannel, Preprocessing, QualityControl", "Author": "Ryan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund\n[aut]", "Maintainer": "Ryan Putney ", "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": "2026-04-28 12:40:39 UTC", "RemoteUrl": "https://github.com/bioc/skewr", "RemoteRef": "HEAD", "RemoteSha": "4e9359b655e1e1ea3c9a9064101ce51e79242f05", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:51:03 UTC", "User": "root" }, "MD5sum": "4c75ceaad21327677c9003a024e807f5", "_user": "bioc", "_type": "src", "_file": "skewr_1.45.0.tar.gz", "_fileid": "4b2b1a740ed7ef1de955a5de2f1c31040c115c7a2dc701eeb37b4108b523d1b1", "_filesize": 1082971, "_sha256": "4b2b1a740ed7ef1de955a5de2f1c31040c115c7a2dc701eeb37b4108b523d1b1", "_created": "2026-05-30T09:51:03.000Z", "_published": "2026-05-30T15:08:17.484Z", "_jobs": [ { "job": 78640851019, "time": 432, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307582095" }, { "job": 78640851039, "time": 645, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307604694" }, { "job": 78640851022, "time": 720, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307610954" }, { "job": 78640851030, "time": 326, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309108714" }, { "job": 78640851026, "time": 437, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309119790" }, { "job": 78639881812, "time": 581, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307317585" }, { "job": 78640851050, "time": 372, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307576430" }, { "job": 78640851052, "time": 491, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307584799" }, { "job": 78640851031, "time": 488, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307584531" }, { "job": 78640851048, "time": 596, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307595971" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676689478", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/skewr", "_commit": { "id": "4e9359b655e1e1ea3c9a9064101ce51e79242f05", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380039 }, "_maintainer": { "name": "Ryan Putney", "email": "ryanputney@gmail.com", "login": "rmputney", "description": "", "uuid": 9374828 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.1", "role": "Depends" }, { "package": "methylumi", "role": "Depends" }, { "package": "wateRmelon", "role": "Depends" }, { "package": "mixsmsn", "role": "Depends" }, { "package": "IlluminaHumanMethylation450kmanifest", "role": "Depends" }, { "package": "minfi", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.19.1", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "GEOquery", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "minfiData", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "dnamethylation", "twochannel", "preprocessing", "qualitycontrol" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 361, "source": "https://www.bioconductor.org/packages/stats/bioc/skewr" }, "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/skewr.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "getBarcodes", "getMethyLumiSet", "getSNparams", "panelPlots", "preprocess", "subsetProbes" ], "_help": [ { "page": "getBarcodes", "title": "Get barcodes from idat file names", "topics": [ "getBarcodes" ] }, { "page": "getMethyLumiSet", "title": "Read idat files and create a 'MethyLumiSet' object", "topics": [ "getMethyLumiSet" ] }, { "page": "getSNparams", "title": "Estimate parameters for finite mixture of Skew-Normal distributions", "topics": [ "getSNparams" ] }, { "page": "panelPlots", "title": "Plot the distributions of the probe intensities and the components of the skew-normal mixture model", "topics": [ "panelPlots" ] }, { "page": "preprocess", "title": "Normalize a MethyLumiSet object using some popular choices", "topics": [ "preprocess" ] }, { "page": "subsetProbes", "title": "Conveniently subset probes by type and retrieve the methylated or unmethylated intensities", "topics": [ "subsetProbes" ] } ], "_rundeps": [ "abind", "affy", "affyio", "annotate", "AnnotationDbi", "askpass", "base64", "beanplot", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "biocmake", "BiocManager", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bumphunter", "cachem", "cigarillo", "cli", "clipr", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "DelayedMatrixStats", "digest", "dir.expiry", "doRNG", "dplyr", "evaluate", "farver", "fastmap", "FDb.InfiniumMethylation.hg19", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "genefilter", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GEOquery", "ggplot2", "glue", "gtable", "h5mread", "HDF5Array", "highr", "hms", "httr", "httr2", "IlluminaHumanMethylation450kanno.ilmn12.hg19", "IlluminaHumanMethylation450kmanifest", "illuminaio", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "lumi", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "methylumi", "mgcv", "mime", "minfi", "mixsmsn", "multtest", "mvtnorm", "nleqslv", "nlme", "nor1mix", "openssl", "org.Hs.eg.db", "pillar", "pkgconfig", "plyr", "png", "preprocessCore", "prettyunits", "progress", "purrr", "quadprog", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RCurl", "readr", "rentrez", "reshape", "reshape2", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "rngtools", "ROC", "Rsamtools", "RSQLite", "rtracklayer", "rvest", "S4Arrays", "S4Vectors", "S7", "scales", "scrime", "selectr", "Seqinfo", "siggenes", "snow", "SparseArray", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "TxDb.Hsapiens.UCSC.hg19.knownGene", "tzdb", "UCSC.utils", "utf8", "vctrs", "viridisLite", "vroom", "wateRmelon", "withr", "xfun", "XML", "xml2", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "skewr.Rnw", "filename": "skewr.pdf", "title": "An Introduction to the skewr Package", "engine": "knitr::knitr", "headings": [], "created": "2015-02-28 00:43:36", "modified": "2018-08-30 17:56:34", "commits": 2 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "skewr", "_universes": [ "bioc", "rmputney" ], "_binaries": [ { "r": "4.7.0", "os": "linux", 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