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Bioinformatics tools for lipidomics data analysis

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QCtool by clipidomics.com

Our own tool for lipidomic quantification and quality control

qctool clipidomics
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LipidSig (offile R package available)

Lipidomics Data Mining Tools, Machine learnining

lipidsig
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LIPID MAPS

Lipidomics Tools Guide

lipidomics tools guide lipidmaps
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Metaboanalyst (offile R package available)

Metabolomics Data Analysis Tools

metaboanalyst
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Metabolomics Workbench

Metabolomics Data Analysis Tools

metabolomicsworkbench
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LION/web

Lipid Ontology Analysis Tools

lion web
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bioPAN

Lipid Pathway Analysis Tools

biopan
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LipiDisease

Lipid Enrychment Analysis on Biomedical Literature Data Tools

lipidisease
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Lipid Mini-On

Lipid Enrychment Analysis Tools

lipid mini on
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LipidHome

Introduction to lipids, blog created and is maintained by William (Bill) W. Christie

Lipidhome
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lipidr Lipidr is 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. 

maplet Maplet (Metabolomics Analysis PipeLinE Toolbox) is an R package for statistical data analysis with a special focus on metabolomics datasets. It allows users to create self-contained analytical pipelines. The toolbox builds upon the bioconductor package SummarizedExperiment (SE), which serves as a central repository for each pipeline’s data, analysis steps, and results. maplet provides a suite of functions for interacting with this container including but not limited to data loading, annotation, statistical analysis, visualization, and reporting. maplet is designed to work with a pipe operator – either the popular %>% operator from the magrittr package or the recently introduced |> from base R. This operator allows for smooth connections between pipeline steps, without the need for temporary variables or multiple assignments. The combination of these elements allows for the creation of pipelines which are simple to follow, highly modular, and easily reproducible.

Skyline MS Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports All Molecules. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale quantitative mass spectrometry studies in life sciences.

LipidXplorer LipidXplorer is the open source software that supports the quantitative characterization of complex lipidomes by interpreting large datasets of shotgun mass spectra. LipidXplorer processes spectra acquired on any type of tandem mass spectrometers; it identifies and quantifies molecular species of any ionizable lipid class by considering any known or assumed molecular fragmentation pathway independently of any resource of reference mass spectra

Rstudio Logo Blue Gray 250 RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Do you have any samples you’d like to analyze?

If you are working on a project and want to complete your results with the lipidomic data, need our advice, analytical support or want to collaborate on one of our active projects, do not hesitate to contact us

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