RMassBank
Workflow to process tandem MS files and build MassBank records
Bioconductor version: Release (3.20)
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("RMassBank")):
Installation
To install this package, start R (version "4.4") 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 | HTML | R Script |
| RMassBank: The workflow by example | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bioinformatics, ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Version | 3.16.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (12 years) |
| License | Artistic-2.0 |
| Depends | 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RMassBank_3.16.0.tar.gz |
| Windows Binary (x86_64) | RMassBank_3.16.0.zip |
| macOS Binary (x86_64) | RMassBank_3.16.0.tgz |
| macOS Binary (arm64) | RMassBank_3.16.0.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 |