Bioinformatics Seminars

Bioinformatics Seminar

Time: 11AM
Venue: Zoom Webinar

26 October 2021

Developing software tools for differential lipidomics analysis

Ahmed Mohamed
WEHI Bioinformatics

The rapid evolution of Mass spectrometry (MS)-based lipidomics has enabled high throughput profiling of numerous lipid classes, uncovering the role of lipids in health and disease. With the rising popularity, public lipidomics datasets are becoming increasingly available. While these public datasets can be mined for potential biological hypotheses, more lipidomic-focussed software tools are required to facilitate data mining of public lipidomics datasets, and to integrate molecular information in differential lipidomics analysis. In this seminar, I present lipidr, an R/Bioconductor package, and a companion web server, LipidSuite, for data mining and analysis of lipidomics datasets. Together, they offer an end-to-end solution for differential lipidomics analysis through a step-by-step workflow for preprocessing, exploration, differential analysis and enrichment analysis of untargeted and targeted lipidomics. To enable interpretation of lipid class, chain length and saturation data, we also developed and implemented a novel Lipid Set Enrichment Analysis. By representing lipidomics datasets as SummarizedExperiment objects, lipidr allow seamless integration with Bioconductor workflows. Additionally, integration with Metabolomics Workbench API, users can directly search, download and reanalyze public lipidomics datasets. Finally, LipidSuite web server allows interactive execution of the analysis workflow, and implements R/Shiny modules that can be reused for similar workflows utilizing the SummarizedExperiment object structure.

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