MassArray

DOI: 10.18129/B9.bioc.MassArray    

Analytical Tools for MassArray Data

Bioconductor version: Release (3.11)

This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.

Author: Reid F. Thompson <reid.thompson at gmail.com>, John M. Greally <john.greally at einstein.yu.edu>

Maintainer: Reid F. Thompson <reid.thompson at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MassArray")

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("MassArray")

 

PDF	R Script	1. Primer
PDF		Reference Manual

Details

biocViews	DNAMethylation, DataImport, Genetics, ImmunoOncology, MassSpectrometry, SNP, Software, Visualization
Version	1.40.0
In Bioconductor since	BioC 2.6 (R-2.11) (10.5 years)
License	GPL (>=2)
Depends	R (>= 2.10.0), methods
Imports	graphics, grDevices, stats, utils
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MassArray_1.40.0.tar.gz
Windows Binary	MassArray_1.40.0.zip
macOS 10.13 (High Sierra)	MassArray_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MassArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MassArray
Package Short Url	https://bioconductor.org/packages/MassArray/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive