lipidr
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see lipidr.
Lipidomics Analysis Workflow in R
Bioconductor version: 3.9
lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of lipidomics data. lipidr parses results exported from Skyline directly into R, allowing integration into current analysis frameworks. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, chain length and unsaturation.
Author: Ahmed Mohamed [cre] 
, Ahmed Mohamed [aut], Jeffrey Molendijk [aut]
Maintainer: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>
citation("lipidr")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lipidr")
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("lipidr")| lipidr_workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Lipidomics, MassSpectrometry, Normalization, QualityControl, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6.0), SummarizedExperiment |
| Imports | methods, stats, utils, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, magrittr |
| System Requirements | |
| URL | https://github.com/ahmohamed/lipidr |
| Bug Reports | https://github.com/ahmohamed/lipidr/issues/ |
See More
| Suggests | knitr, rmarkdown, BiocStyle, ggrepel, plotly, covr, spelling |
| Linking To | |
| 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 | lipidr_1.0.0.tar.gz |
| Windows Binary | lipidr_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | lipidr_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/lipidr |
| Source Repository (Developer Access) | git clone [email protected]:packages/lipidr |
| Bioc Package Browser | https://code.bioconductor.org/browse/lipidr/ |
| Package Short Url | https://bioconductor.org/packages/lipidr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |