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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")
RMassBank non-standard usage PDF R Script
RMassBank using XCMS walkthrough PDF R Script
RMassBank walkthrough PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 2.12.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends Rcpp
Imports XML, RCurl, rjson, S4Vectors, digest, rcdk, yaml, mzR, methods, Biobase, MSnbase, httr
System Requirements OpenBabel
URL
See More
Suggests gplots, RMassBankData, xcms(>= 1.37.1), CAMERA, RUnit, enviPat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me RMassBankData
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/RMassBank/
Package Short Url https://bioconductor.org/packages/RMassBank/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive