1 Introduction | 2 Quick start | 3 Example using presummarized DNA Methylation array data | 4 Example using 450k data downloaded from The Cancer Genome Atlas | 5 Example using 450k data downloaded from GEO | 6 Parallel summarization | 7 Customize MethylAid | 8 Session info
Package: MethylAid 1.47.0
L.J.Sinke
MethylAid: Visual and interactive quality control of large Illumina DNA Methylation array data sets
A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
Authors:
MethylAid_1.47.0.tar.gz
MethylAid_1.47.0.zip(r-4.7)MethylAid_1.47.0.zip(r-4.6)MethylAid_1.47.0.zip(r-4.5)
MethylAid_1.47.0.tgz(r-4.6-any)MethylAid_1.47.0.tgz(r-4.5-any)
MethylAid_1.47.0.tar.gz(r-4.7-any)MethylAid_1.47.0.tar.gz(r-4.6-any)
MethylAid_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MethylAid/json (API)
| # Install 'MethylAid' in R: |
| install.packages('MethylAid', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- exampleData - SummarizedData object on 500 450k Human Methylation samples
On BioConductor:MethylAid-1.47.0(bioc 3.24)MethylAid-1.46.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dnamethylationmethylationarraymicroarraytwochannelqualitycontrolbatcheffectvisualizationgui
Last updated from:33390607af. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 528 | ||
| linux-devel-x86_64 | OK | 880 | ||
| source / vignettes | OK | 713 | ||
| linux-release-x86_64 | OK | 862 | ||
| macos-release-arm64 | OK | 656 | ||
| macos-oldrel-arm64 | OK | 617 | ||
| windows-devel | OK | 896 | ||
| windows-release | OK | 938 | ||
| windows-oldrel | OK | 857 | ||
| wasm-release | OK | 544 |
Exports:combineshowsummarizevisualize
Dependencies:abindannotateAnnotationDbiaskpassbase64base64encbeanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbslibbumphuntercachemcigarilloclicliprcodetoolscommonmarkcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrfarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegridBasegtableh5mreadHDF5Arrayhexbinhmshtmltoolshttpuvhttrhttr2illuminaioIRangesisobanditeratorsjquerylibjsonliteKEGGRESTlabelinglambda.rlaterlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslotelpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspromisespurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7sassscalesscrimeselectrSeqinfoshinysiggenessnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| generate background data | as.background as.background,summarizedData-method |
| concatenates two summarizedData objects into one object | combine,summarizedData,ANY-method |
| summarizedData object on 500 450k Human Methylation samples | exampleData |
| show method for Illumina Human DNA Methylation array data | show,summarizedData-method |
| summarization of Illumina Human DNA Methylation array data | summarize |
| container for summarized Illumina Human DNA Methylation array data | summarizedData-class |
| visualize the summarized Illumina Human DNA Methylation array data | visualize visualize,summarizedData-method |
