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DESCRIPTION
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DESCRIPTION
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Package: MethylAid
Type: Package
Title: Visual and interactive quality control of large Illumina DNA
Methylation array data sets
Version: 1.39.0
Date: 2019-10-07
Authors@R: c(person("Maarten", "van Iterson",
email="mviterson@gmail.com", role="cre"),
person("Elmar", "Tobi", role="ctb"),
person("Roderick", "Slieker", role="ctb"),
person("Wouter", "den Hollander", role="ctb"),
person("Rene", "Luijk", role="ctb"),
person("Bas", "Heijmans", role="ctb"))
Author: Maarten van Iterson [aut, cre], Elmar Tobi[ctb],
Roderick Slieker[ctb], Wouter den Hollander[ctb],
Rene Luijk[ctb] and Bas Heijmans[ctb]
Maintainer: L.J.Sinke <L.J.Sinke@lumc.nl>
Description: 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.
License: GPL (>= 2)
VignetteBuilder: knitr
biocViews: DNAMethylation,
MethylationArray,
Microarray,
TwoChannel,
QualityControl,
BatchEffect,
Visualization,
GUI
Depends:
R (>= 3.4)
Imports:
Biobase,
BiocParallel,
BiocGenerics,
ggplot2,
grid,
gridBase,
grDevices,
graphics,
hexbin,
matrixStats,
minfi (>= 1.22.0),
methods,
RColorBrewer,
shiny,
stats,
SummarizedExperiment,
utils
Suggests:
BiocStyle,
knitr,
MethylAidData,
minfiData,
minfiDataEPIC,
RUnit
RoxygenNote: 6.0.1