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lipidr: A Software Tool for Data Mining and Analysis of Lipidomics Datasets
journal contribution
posted on 2020-03-23, 11:34 authored by Ahmed Mohamed, Jeffrey Molendijk, Michelle M. HillThe rapid evolution
of mass spectrometry (MS)-based lipidomics
has enabled the simultaneous measurement of numerous lipid classes.
With lipidomics datasets becoming increasingly available, lipidomic-focused
software tools are required to facilitate data analysis as well as
mining of public datasets, integrating lipidomics-unique molecular
information such as lipid class, chain length, and unsaturation. To
address this need, we developed lipidr, an open-source
R/Bioconductor package for data mining and analysis of lipidomics
datasets. lipidr implements a comprehensive lipidomic-focused
analysis workflow for targeted and untargeted lipidomics. lipidr imports numerical matrices, Skyline exports, and
Metabolomics Workbench files directly into R, automatically inferring
lipid class and chain information from lipid names. Through integration
with the Metabolomics Workbench API, users can search, download, and
reanalyze public lipidomics datasets seamlessly. lipidr allows thorough data inspection, normalization, and uni- and multivariate
analyses, displaying results as interactive visualizations. To enable
interpretation of lipid class, chain length, and total unsaturation
data, we also developed and implemented a novel lipid set enrichment
analysis. A companion online guide with two live example datasets
is presented at https://www.lipidr.org/. We expect that the ease of use and innovative features of lipidr will allow the lipidomics research community to gain
novel detailed insights from lipidomics data.