Package: skewr 1.39.0

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]

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skewr.pdf |skewr.html✨
skewr/json (API)

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

Peer review:

On BioConductor:skewr-1.39.0(bioc 3.21)skewr-1.38.0(bioc 3.20)

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 200 downloads 6 exports 166 dependencies

Last updated 2 months agofrom:d7cf1edea3. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:getBarcodesgetMethyLumiSetgetSNparamspanelPlotspreprocesssubsetProbes

Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrevaluatefansifarverfastmapFDb.InfiniumMethylation.hg19foreachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableHDF5Arrayhighrhmshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestilluminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlumimagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimixsmsnmulttestmunsellmvtnormnleqslvnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsROCRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwateRmelonwithrxfunXMLxml2xtableXVectoryamlzlibbioc

An Introduction to the skewr Package

Rendered fromskewr.Rnwusingknitr::knitron Oct 31 2024.

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