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RMassBank

Workflow to process tandem MS files and build MassBank records

Bioconductor version: 3.23 · Package version: 3.22.0

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.

Installation

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

BiocManager::install("RMassBank")

Details

MaintainerRMassBank at Eawag <massbank@eawag.ch>
AuthorMichael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, Paul Stahlhofen, Tobias Schulze with contributions of Hendrik Treutler
LicenseArtistic-2.0
System RequirementsOpenBabel
Downloads rank731
Source branchRELEASE_3_23
biocViewsBioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageRMassBank_3.22.0.tar.gz
Windows binary (x86_64)RMassBank_3.22.0.zip
macOS binary (arm64)RMassBank_3.22.0.tgz
macOS binary (x86_64)RMassBank_3.22.0.tgz
Dependencies

Depends: R (>= 4.1.0), Rcpp

Imports: assertthat, Biobase, ChemmineR, data.table, digest, dplyr, enviPat, glue, httr, httr2, logger, methods, MSnbase, mzR, purrr, R.utils, rcdk, readJDX, readr, rjson, S4Vectors, tibble, tidyselect, webchem, XML, yaml

Suggests: BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown, RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1)

Reverse dependencies

Suggests Me (1): RMassBankData