To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

RMassBank

 

   

Workflow to process tandem MS files and build MassBank records

Bioconductor version: Release (3.3)

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>

Citation (from within R, enter citation("RMassBank")):

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 2.0.0
In Bioconductor since BioC 2.11 (R-2.15) (3.5 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.

Package Source RMassBank_2.0.0.tar.gz
Windows Binary RMassBank_2.0.0.zip
Mac OS X 10.9 (Mavericks) RMassBank_2.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/RMassBank/tree/release-3.3
Package Short Url http://bioconductor.org/packages/RMassBank/
Package Downloads Report Download Stats

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