RMassBank

DOI: 10.18129/B9.bioc.RMassBank  

Workflow to process tandem MS files and build MassBank records

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

HTML	R Script	RMassBank for XCMS
HTML	R Script	RMassBank: Non-standard usage
HTML	R Script	RMassBank: The workflow by example
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	3.8.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 years)
License	Artistic-2.0
Depends	Rcpp
Imports	XML, rjson, S4Vectors, digest, rcdk, yaml, mzR, methods, Biobase, MSnbase, httr, enviPat, assertthat, logger, RCurl, readJDX, webchem, ChemmineR, ChemmineOB, R.utils, data.table
LinkingTo
Suggests	BiocStyle, gplots, RMassBankData(>= 1.33.1), xcms(>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown
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_3.8.0.tar.gz
Windows Binary	RMassBank_3.8.0.zip
macOS Binary (x86_64)	RMassBank_3.8.0.tgz
macOS Binary (arm64)
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