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RMassBank

Workflow to process tandem MS files and build MassBank records


Bioconductor version: Release (3.18)

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

Details

biocViews Bioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 3.12.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends Rcpp
Imports XML, rjson, S4Vectors, digest, rcdk, yaml, mzR, methods, Biobase, MSnbase, httr, enviPat, assertthat, logger, readJDX, webchem, ChemmineR, ChemmineOB, R.utils, data.table, glue
System Requirements OpenBabel
URL
See More
Suggests BiocStyle, gplots, RMassBankData(>= 1.33.1), xcms(>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown
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_3.12.0.tar.gz
Windows Binary RMassBank_3.12.0.zip
macOS Binary (x86_64) RMassBank_3.12.0.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