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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MassArray")
In most cases, you don't need to download the package archive at all.
MassArray
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This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see MassArray.
Analytical Tools for MassArray Data
Bioconductor version: 3.1
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 <rthompso at aecom.yu.edu>, John M. Greally <jgreally at aecom.yu.edu>
Maintainer: Reid F. Thompson <rthompso at aecom.yu.edu>
Citation (from within R,
enter citation("MassArray")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MassArray")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MassArray")
| R Script | 1. Primer | |
| Reference Manual |
Details
| biocViews | DNAMethylation, DataImport, Genetics, MassSpectrometry, SNP, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (6 years) |
| License | GPL (>=2) |
| Depends | R (>= 2.10.0), methods |
| Imports | graphics, grDevices, methods, stats, utils |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MassArray_1.20.0.tar.gz |
| Windows Binary | MassArray_1.20.0.zip |
| Mac OS X 10.6 (Snow Leopard) | MassArray_1.20.0.tgz |
| Mac OS X 10.9 (Mavericks) | MassArray_1.20.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/MassArray/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/MassArray/ |
| Package Downloads Report | Download Stats |
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