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rgoslin

Lipid Shorthand Name Parsing and Normalization


Bioconductor version: Release (3.18)

The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.

Author: Nils Hoffmann [aut, cre] , Dominik Kopczynski [aut]

Maintainer: Nils Hoffmann <nils.hoffmann at cebitec.uni-bielefeld.de>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("rgoslin")

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("rgoslin")
Using R Goslin to parse and normalize lipid nomenclature HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Lipidomics, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends
Imports Rcpp (>= 1.0.3), dplyr
System Requirements
URL https://github.com/lifs-tools/rgoslin
Bug Reports https://github.com/lifs-tools/rgoslin/issues
See More
Suggests testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package rgoslin_1.6.0.tar.gz
Windows Binary rgoslin_1.6.0.zip
macOS Binary (x86_64) rgoslin_1.6.0.tgz
macOS Binary (arm64) rgoslin_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rgoslin
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rgoslin
Bioc Package Browser https://code.bioconductor.org/browse/rgoslin/
Package Short Url https://bioconductor.org/packages/rgoslin/
Package Downloads Report Download Stats