MassArray
Analytical Tools for MassArray Data
Bioconductor version: 3.24 · Package version: 1.65.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MassArray")Details
| Maintainer | Reid F. Thompson <reid.thompson@gmail.com> |
| Author | Reid F. Thompson <reid.thompson@gmail.com>, John M. Greally <john.greally@einstein.yu.edu> |
| License | GPL (>=2) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DataImport, Genetics, ImmunoOncology, MassSpectrometry, SNP, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/MassArray/ |
Citation
From within R, enter citation("MassArray"):
Reid F. Thompson, John M. Greally. MassArray: Analytical Tools for MassArray Data. doi:10.18129/B9.bioc.MassArray, R package version 1.65.0, https://bioconductor.org/packages/MassArray.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MassArray_1.65.0.tar.gz |
| Windows binary (x86_64) | MassArray_1.65.0.zip |
| macOS binary (arm64) | MassArray_1.65.0.tgz |
| macOS binary (x86_64) | MassArray_1.65.0.tgz |
Dependencies
Depends: R (>= 2.10.0), methods
Imports: graphics, grDevices, stats, utils