RMassBank

DOI: 10.18129/B9.bioc.RMassBank    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RMassBank.

Workflow to process tandem MS files and build MassBank records

Bioconductor version: 3.9

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 (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RMassBank")

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("RMassBank")

 

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

Details

biocViews	Bioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	2.12.0
In Bioconductor since	BioC 2.11 (R-2.15) (7 years)
License	Artistic-2.0
Depends	Rcpp
Imports	XML, RCurl, rjson, S4Vectors, digest, rcdk, yaml, mzR, methods, Biobase, MSnbase, httr
LinkingTo
Suggests	gplots, RMassBankData, xcms(>= 1.37.1), CAMERA, RUnit, enviPat
SystemRequirements	OpenBabel
Enhances
URL
Depends On Me
Imports Me
Suggests Me	RMassBankData
Links To Me
Build Report

Package Archives

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

Source Package	RMassBank_2.12.0.tar.gz
Windows Binary	RMassBank_2.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	RMassBank_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RMassBank
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RMassBank
Package Short Url	https://bioconductor.org/packages/RMassBank/
Package Downloads Report	Download Stats