MethylAid
This is the development version of MethylAid; for the stable release version, see MethylAid.
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Bioconductor version: Development (3.24)
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: L.J.Sinke <L.J.Sinke at lumc.nl>
citation("MethylAid")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MethylAid")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MethylAid")| MethylAid: Visual and Interactive quality control of Illumina Human DNA Methylation array data | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL (>= 2) |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit |
| Linking To | |
| Enhances | |
| Depends On Me | MethylAidData |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MethylAid_1.47.0.tar.gz |
| Windows Binary (x86_64) | MethylAid_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | MethylAid_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | MethylAid_1.47.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MethylAid |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MethylAid |
| Bioc Package Browser | https://code.bioconductor.org/browse/MethylAid/ |
| Package Short Url | https://bioconductor.org/packages/MethylAid/ |
| Package Downloads Report | Download Stats |