Package: skewr 1.44.0

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_1.44.0.tar.gz
skewr_1.44.0.zip(r-4.7)skewr_1.44.0.zip(r-4.6)skewr_1.44.0.zip(r-4.5)
skewr_1.44.0.tgz(r-4.6-any)skewr_1.44.0.tgz(r-4.5-any)
skewr_1.44.0.tar.gz(r-4.7-any)skewr_1.44.0.tar.gz(r-4.6-any)
skewr_1.44.0.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-release.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 3 scripts 361 downloads 6 exports 167 dependencies

Last updated from:33814cea58 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR419
linux-devel-x86_64NOTE741
source / vignettesOK535
linux-release-x86_64NOTE655
macos-release-arm64NOTE488
macos-oldrel-arm64NOTE401
windows-develNOTE590
windows-releaseNOTE493
windows-oldrelNOTE500
wasm-releaseOK377

Exports:getBarcodesgetMethyLumiSetgetSNparamspanelPlotspreprocesssubsetProbes

Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicliprcodetoolscpp11crayoncurldata.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