MassArray
This is the development version of MassArray; for the stable release version, see MassArray.
Analytical Tools for MassArray Data
Bioconductor version: Development (3.24)
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>
citation("MassArray")):
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("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")| 1. Primer | R Script | |
| Reference Manual |
Details
| biocViews | DNAMethylation, DataImport, Genetics, ImmunoOncology, MassSpectrometry, SNP, Software, Visualization |
| Version | 1.65.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (16.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 2.10.0), methods |
| Imports | graphics, grDevices, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | MassArray_1.65.0.tar.gz |
| Windows Binary (x86_64) | MassArray_1.65.0.zip |
| macOS Binary (big-sur-x86_64) | MassArray_1.65.0.tgz |
| macOS Binary (sonoma-arm64) | MassArray_1.65.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MassArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MassArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/MassArray/ |
| Package Short Url | https://bioconductor.org/packages/MassArray/ |
| Package Downloads Report | Download Stats |