msPurity
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see msPurity.
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Bioconductor version: 3.8
Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called "precursor purity". Also provides simple processing steps (averaging, filtering, blank subtraction, etc) for DI-MS data. Works for both LC-MS(/MS) and DI-MS(/MS) data. Spectral matching of fragmentation spectra can also be run against a SQLite database of library spectra.
Author: Thomas N. Lawson, Ralf Weber, Martin Jones, Mark Viant, Warwick Dunn
Maintainer: Thomas N. Lawson <thomas.nigel.lawson at gmail.com>
citation("msPurity")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("msPurity")
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("msPurity")| msPurity | HTML | R Script |
| msPurity spectral matching | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Version | 1.8.1 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | GPL (>= 2) |
| Depends | Rcpp |
| Imports | plyr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite |
| System Requirements | |
| URL |
See More
| Suggests | testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA |
| 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 | msPurity_1.8.1.tar.gz |
| Windows Binary | msPurity_1.8.1.zip |
| Mac OS X 10.11 (El Capitan) | msPurity_1.8.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/msPurity |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/msPurity |
| Bioc Package Browser | https://code.bioconductor.org/browse/msPurity/ |
| Package Short Url | https://bioconductor.org/packages/msPurity/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |