RMassBank

This is the development version of RMassBank; for the stable release version, see RMassBank.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11

Workflow to process tandem MS files and build MassBank records

Bioconductor version: Development (3.24)

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, Paul Stahlhofen, Tobias Schulze with contributions of Hendrik Treutler

Maintainer: RMassBank at Eawag <massbank at eawag.ch>

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

Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, Paul Stahlhofen, Tobias Schulze with contributions of Hendrik Treutler. RMassBank: Workflow to process tandem MS files and build MassBank records. doi:10.18129/B9.bioc.RMassBank, R package version 3.23.0, https://bioconductor.org/packages/RMassBank.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	HTML	R Script
RMassBank: The workflow by example	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	3.23.0
In Bioconductor since	BioC 2.11 (R-2.15) (14 years)
License	Artistic-2.0
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
System Requirements	OpenBabel
URL

Suggests	BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown, RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	RMassBankData
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	RMassBank_3.23.0.tar.gz
Windows Binary (x86_64)	RMassBank_3.23.0.zip
macOS Binary (big-sur-x86_64)	RMassBank_3.23.0.tgz
macOS Binary (sonoma-arm64)	RMassBank_3.23.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RMassBank
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RMassBank
Package Short Url	https://bioconductor.org/packages/RMassBank/
Package Downloads Report	Download Stats