RMassBank

DOI: 10.18129/B9.bioc.RMassBank    

Workflow to process tandem MS files and build MassBank records

Bioconductor version: Release (3.6)

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Author: Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze

Maintainer: RMassBank at Eawag <massbank at eawag.ch>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RMassBank")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RMassBank")

 

PDF	R Script	RMassBank non-standard usage
PDF	R Script	RMassBank using XCMS walkthrough
PDF	R Script	RMassBank walkthrough
PDF		Reference Manual

Details

biocViews	Bioinformatics, MassSpectrometry, Metabolomics, Software
Version	2.6.0
In Bioconductor since	BioC 2.11 (R-2.15) (5.5 years)
License	Artistic-2.0
Depends	Rcpp
Imports	XML, RCurl, rjson, S4Vectors, digest, rcdk, yaml, mzR, methods, Biobase, MSnbase
LinkingTo
Suggests	gplots, RMassBankData, xcms(>= 1.37.1), CAMERA, ontoCAT, RUnit, enviPat
SystemRequirements	OpenBabel
Enhances
URL
Depends On Me
Imports Me
Suggests Me	RMassBankData
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RMassBank_2.6.0.tar.gz
Windows Binary	RMassBank_2.6.0.zip
Mac OS X 10.11 (El Capitan)	RMassBank_2.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RMassBank
Package Short Url	http://bioconductor.org/packages/RMassBank/
Package Downloads Report	Download Stats