Package: shinyMethyl 1.43.0

Jean-Philippe Fortin

shinyMethyl: Interactive visualization for Illumina methylation arrays

Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

Authors:Jean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut]

shinyMethyl_1.43.0.tar.gz
shinyMethyl_1.43.0.zip(r-4.5)shinyMethyl_1.43.0.zip(r-4.4)shinyMethyl_1.43.0.zip(r-4.3)
shinyMethyl_1.43.0.tgz(r-4.4-any)shinyMethyl_1.43.0.tgz(r-4.3-any)
shinyMethyl_1.43.0.tar.gz(r-4.5-noble)shinyMethyl_1.43.0.tar.gz(r-4.4-noble)
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shinyMethyl.pdf |shinyMethyl.html✨
shinyMethyl/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/jfortin1/shinymethyl/issues

On BioConductor:shinyMethyl-1.43.0(bioc 3.21)shinyMethyl-1.42.0(bioc 3.20)

dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarray

7.42 score 5 stars 38 scripts 422 downloads 18 mentions 16 exports 148 dependencies

Last updated 23 days agofrom:9722e5385b. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winNOTENov 19 2024
R-4.5-linuxNOTENov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

Exports:combinegetBetagetCNgetGreenControlsgetMgetMethgetPCAgetRedControlsgetUnmethorderByNamepDatarunShinyMethylsampleNamesshinyMethylSetshinySummarizeshow

Dependencies:abindannotateAnnotationDbiaskpassbase64base64encbeanplotBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbslibbumphuntercachemclicliprcodetoolscommonmarkcpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrfansifastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueHDF5Arrayhmshtmltoolshttpuvhttrhttr2illuminaioIRangesiteratorsjquerylibjsonliteKEGGRESTlambda.rlaterlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspromisespurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorssassscrimeselectrshinysiggenessnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2xtableXVectoryamlzlibbioc

shinyMethyl: interactive visualization of Illumina 450K methylation arrays

Jean-Philippe Fortin, Kasper Daniel Hansen

Rendered fromshinyMethyl.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-11-27
Started: 2022-11-27

Readme and manuals

Help Manual

Help pageTopics
Run the interactive shinyMethyl sessionrunShinyMethyl
shinyMethylSet instancescombine combine,shinyMethylSet,shinyMethylSet-method getBeta getBeta,shinyMethylSet-method getCN getCN,shinyMethylSet-method getGreenControls getM getM,shinyMethylSet-method getMeth getMeth,shinyMethylSet-method getPCA getRedControls getUnmeth getUnmeth,shinyMethylSet-method orderByName pData pData,shinyMethylSet-method sampleNames sampleNames,shinyMethylSet-method shinyMethylSet shinyMethylSet-class show,shinyMethylSet-method
Summarizing a large 450K experiment into a shinyMethylSetshinySummarize shinySummarize,GenomicRatioSet-method shinySummarize,RGChannelSet-method shinySummarize-methods