lipidr-package: Analysis workflow for targeted lipidomics

lipidr-packageR Documentation

Analysis workflow for targeted lipidomics


lipidr implements a series of functions to facilitate inspection, analysis and visualization of targeted lipidomics datasets. lipidr takes exported Skyline CSV as input, allowing for multiple methods to be analyzed together.


lipidr represents Skyline files as SummarizedExperiment objects, which can easily be integrated with a wide variety of Bioconductor packages. Sample annotations, such as sample group or other clinical information can be loaded. lipidr generates various plots, such as PCA score plots and box plots, for quality control of samples and measured lipids. Normalization methods with and without internal standards are also supported.

Differential analysis can be performed using any of the loaded clinical variables, which can be readily visualized as volcano plots. A novel lipid set enrichment analysis (LSEA) is implemented to detect preferential enrichment of certain lipid classes, total chain lengths or unsaturation patterns. Plots for the visualization of enrichment results are also implemented.


Ahmed Mohamed

ahmohamed/lipidr documentation built on Aug. 17, 2022, 1:35 a.m.