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biocLite("MassArray")
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MassArray
Analytical Tools for MassArray Data
Bioconductor version: 3.0
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:
source("http://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 | 1.18.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) |
| 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_1.18.0.tar.gz |
| Windows Binary | MassArray_1.18.0.zip |
| Mac OS X 10.6 (Snow Leopard) | MassArray_1.18.0.tgz |
| Mac OS X 10.9 (Mavericks) | MassArray_1.18.0.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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