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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethylAid")
In most cases, you don't need to download the package archive at all.
MethylAid
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Visual and interactive quality control of large Illumina DNA Methylation array data sets
Bioconductor version: Release (3.3)
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.
Author: Maarten van Iterson [aut, cre], Elmar Tobi[ctb], Roderick Slieker[ctb], Wouter den Hollander[ctb], Rene Luijk[ctb] and Bas Heijmans[ctb]
Maintainer: M. van Iterson <mviterson at gmail.com>
Citation (from within R,
enter citation("MethylAid")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethylAid")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MethylAid")
| R Script | MethylAid: Visual and Interactive quality control of Illumina Human DNA Methylation array data | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BatchEffect, DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization |
| Version | 1.6.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0) |
| Imports | Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi(>= 1.17.9), methods, RColorBrewer, shiny, stats, utils |
| LinkingTo | |
| Suggests | BiocStyle, knitr, MethylAidData, minfiData, RUnit |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/mvaniterson/methylaid |
| BugReports | https://github.com/mvaniterson/methylaid/issues |
| Depends On Me | MethylAidData |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MethylAid_1.6.2.tar.gz |
| Windows Binary | MethylAid_1.6.2.zip |
| Mac OS X 10.9 (Mavericks) | MethylAid_1.6.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/MethylAid/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/MethylAid/ |
| Package Downloads Report | Download Stats |
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