lipidr

DOI: 10.18129/B9.bioc.lipidr    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see lipidr.

Data Mining and Analysis of Lipidomics Datasets

Bioconductor version: 3.12

lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. 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, total chain length and unsaturation.

Author: Ahmed Mohamed [cre] , Ahmed Mohamed [aut], Jeffrey Molendijk [aut]

Maintainer: Ahmed Mohamed <mohamed at kuicr.kyoto-u.ac.jp>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	lipidr_workflow
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Lipidomics, MassSpectrometry, Normalization, QualityControl, Software, Visualization
Version	2.4.0
In Bioconductor since	BioC 3.9 (R-3.6) (2 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0), SummarizedExperiment
Imports	methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr, spelling, testthat
SystemRequirements
Enhances
URL	https://github.com/ahmohamed/lipidr
BugReports	https://github.com/ahmohamed/lipidr/issues/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	lipidr_2.4.0.tar.gz
Windows Binary	lipidr_2.4.0.zip
macOS 10.13 (High Sierra)	lipidr_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/lipidr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/lipidr
Package Short Url	https://bioconductor.org/packages/lipidr/
Package Downloads Report	Download Stats