rgoslin
This is the development version of rgoslin; for the stable release version, see rgoslin.
Lipid Shorthand Name Parsing and Normalization
Bioconductor version: Development (3.24)
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("rgoslin")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Lipidomics, MassSpectrometry, Metabolomics, Normalization, Preprocessing, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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 | MetMashR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rgoslin_1.17.0.tar.gz |
| Windows Binary (x86_64) | rgoslin_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | rgoslin_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | rgoslin_1.17.0.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 |