Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00098892%3A_____%2F25%3A10159454" target="_blank" >RIV/00098892:_____/25:10159454 - isvavai.cz</a>
Result on the web
<a href="https://www.nature.com/articles/s41467-025-63751-1" target="_blank" >https://www.nature.com/articles/s41467-025-63751-1</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s41467-025-63751-1" target="_blank" >10.1038/s41467-025-63751-1</a>

Result language
angličtina
Original language name
Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data
Original language description
Mass spectrometry-based lipidomics and metabolomics generate extensive data sets that, along with metadata such as clinical parameters, require specific data exploration skills to identify and visualize statistically significant trends and biologically relevant differences. Besides tailored methods developed by individual labs, a solid core of freely accessible tools exists for exploratory data analysis and visualization, which we have compiled here, including preparation of descriptive statistics, annotated box plots, hypothesis testing, volcano plots, lipid maps and fatty acyl chain plots, unsupervised and supervised dimensionality reduction, dendrograms, and heat maps. This review is intended for those who would like to develop their skills in data analysis and visualization using freely available R or Python solutions. Beginners are guided through a selection of R and Python libraries for producing publication-ready graphics without being overwhelmed by the code complexity. This manuscript, along with associated GitBook code repository containing step-by-step instructions, offers readers a comprehensive guide, encouraging the application of R and Python for robust and reproducible chemometric analysis of omics data.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
20602 - Medical laboratory technology (including laboratory samples analysis; diagnostic technologies) (Biomaterials to be 2.9 [physical characteristics of living material as related to medical implants, devices, sensors])

Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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