Package: skewr 1.45.0

Ryan Putney

skewr: Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of 'tick' marks located above the x-axis.

Authors:Ryan Putney [cre, aut], Steven Eschrich [aut], Anders Berglund [aut]

skewr_1.45.0.tar.gz
skewr_1.45.0.zip(r-4.7)skewr_1.45.0.zip(r-4.6)skewr_1.45.0.zip(r-4.5)
skewr_1.45.0.tgz(r-4.6-any)skewr_1.45.0.tgz(r-4.5-any)
skewr_1.45.0.tar.gz(r-4.7-any)skewr_1.45.0.tar.gz(r-4.6-any)
skewr_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
skewr/json (API)

# Install 'skewr' in R:
install.packages('skewr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:skewr-1.45.0(bioc 3.24)skewr-1.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylationtwochannelpreprocessingqualitycontrol

3.30 score 9 scripts 361 downloads 6 exports 168 dependencies

Last updated from:4e9359b655. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR432
linux-devel-x86_64NOTE645
source / vignettesOK581
linux-release-x86_64NOTE720
macos-release-arm64NOTE437
macos-oldrel-arm64NOTE326
windows-develNOTE491
windows-releaseNOTE596
windows-oldrelNOTE488
wasm-releaseOK372

Exports:getBarcodesgetMethyLumiSetgetSNparamspanelPlotspreprocesssubsetProbes

Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrevaluatefarverfastmapFDb.InfiniumMethylation.hg19filelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableh5mreadHDF5Arrayhighrhmshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestilluminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlumimagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimixsmsnmulttestmvtnormnleqslvnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsROCRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwateRmelonwithrxfunXMLxml2xtableXVectoryaml

An Introduction to the skewr Package

Rendered fromskewr.Rnwusingknitr::knitron May 30 2026.

Last update: 2018-08-30
Started: 2015-02-28