shinyMethyl: Interactive visualization for Illumina methylation arrays
Version 1.12.0

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

AuthorJean-Philippe Fortin [cre, aut], Kasper Daniel Hansen [aut]
Bioconductor views DNAMethylation Microarray Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerJean-Philippe Fortin <jfortin@jhsph.edu>
LicenseArtistic-2.0
Version1.12.0
URL https://github.com/Jfortin1/shinyMethyl
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("shinyMethyl")

Getting started

Package overview
README.md

Popular man pages

runShinyMethyl: Run the interactive shinyMethyl session
shinyMethyl-package: Interactive visualization for Illumina methylation arrays
shinyMethylSet-class: shinyMethylSet instances
shinySummarize-methods: Summarizing a large 450K experiment into a shinyMethylSet
See all...

All man pages Function index File listing

Man pages

runShinyMethyl: Run the interactive shinyMethyl session
shinyMethyl-package: Interactive visualization for Illumina methylation arrays
shinyMethylSet-class: shinyMethylSet instances
shinySummarize-methods: Summarizing a large 450K experiment into a shinyMethylSet

Functions

addHoverDensity Source code
addHoverPoints Source code
addHoverQC Source code
buildColors Source code
checkSex Source code
combine Man page
combine,shinyMethylSet,shinyMethylSet-method Man page
densitiesPlot Source code
getBeta Man page
getBeta,shinyMethylSet-method Man page
getCN Man page
getCN,shinyMethylSet-method Man page
getGreenControls Man page Source code
getM Man page
getM,shinyMethylSet-method Man page
getMeth Man page
getMeth,shinyMethylSet-method Man page
getPCA Man page Source code
getRedControls Man page Source code
getUnmeth Man page
getUnmeth,shinyMethylSet-method Man page
orderByName Man page Source code
pData Man page
pData,shinyMethylSet-method Man page
plotDesign450k Source code
plotDiscrepancyGenders Source code
plotInternalControls Source code
plotLegendDesign450k Source code
plotPCA Source code
plotPlate Source code
plotPredictedGender Source code
plotQC Source code
plotRow Source code
returnControlStat Source code
returnGivenGender Source code
returnPredictedGender Source code
runShinyMethyl Man page Source code
sampleNames Man page
sampleNames,shinyMethylSet-method Man page
server.shinyMethyl Source code
shinyCombine Source code
shinyMethyl Man page
shinyMethyl-package Man page
shinyMethylSet Man page Source code
shinyMethylSet-class Man page
shinySummarize Man page
shinySummarize,GenomicRatioSet-method Man page
shinySummarize,RGChannelSet-method Man page
shinySummarize-methods Man page
show,shinyMethylSet-method Man page
ui.shinyMethyl Source code

Files

.travis.yml
DESCRIPTION
NAMESPACE
R
R/plotControlProbes.R
R/plotDensities.R
R/plotDesign.R
R/plotPCA.R
R/plotQC.R
R/plotSex.R
R/runShinyMethyl.R
R/server.R
R/shinyMethylSet.R
R/shinySummarize.R
R/ui.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/shinyMethyl.R
inst/doc/shinyMethyl.Rnw
inst/doc/shinyMethyl.pdf
inst/testData
inst/testData/testData.R
inst/unitTests
inst/unitTests/testDigests.rda
inst/unitTests/test_shinySummarize.R
man
man/runShinyMethyl.Rd
man/shinyMethyl-package.Rd
man/shinyMethylSet-class.Rd
man/shinySummarize-methods.Rd
tests
tests/runTests.R
vignettes
vignettes/figures
vignettes/figures/All.png
vignettes/figures/BothPlate.pdf
vignettes/figures/BothStatus.pdf
vignettes/screenshot_design.png
vignettes/screenshot_designbias.png
vignettes/screenshot_pca.png
vignettes/screenshot_qc.png
vignettes/screenshot_sexprediction.png
vignettes/shinyMethyl.Rnw
vignettes/shinyMethyl.bib
shinyMethyl documentation built on May 20, 2017, 10:10 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.