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source("http://bioconductor.org/biocLite.R")
biocLite("MethylAid")
In most cases, you don't need to download the package archive at all.
MethylAid
Visual and interactive quality control of large Illumina 450k data sets
Bioconductor version: 3.0
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, Elmar. Tobi, Roderick Slieker, Wouter den Hollander, Rene Luijk and Bas Heijmans
Maintainer: M. van Iterson <m.van_iterson at lumc.nl>
Citation (from within R,
enter citation("MethylAid")):
Installation
To install this package, start R and enter:
source("http://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 large Illumina 450k data sets | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, GUI, MethylationArray, Microarray, QualityControl, Software, TwoChannel, Visualization |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0) |
| Imports | methods, matrixStats, BiocParallel, shiny, ggplot2, RColorBrewer, minfi, IlluminaHumanMethylation450kmanifest, FDb.InfiniumMethylation.hg19 |
| LinkingTo | |
| Suggests | BiocStyle, RUnit, BiocGenerics, minfiData, knitr |
| SystemRequirements | |
| Enhances | |
| URL | http://shiny.bioexp.nl/MethylAid |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MethylAid_1.0.2.tar.gz |
| Windows Binary | MethylAid_1.0.2.zip |
| Mac OS X 10.6 (Snow Leopard) | MethylAid_1.0.2.tgz |
| Mac OS X 10.9 (Mavericks) | MethylAid_1.0.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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