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.

Department of Analytical Chemistry Faculty of Chemical Technology University of Pardubice Pardubice Czechia

Department of Biomedical Engineering Faculty of Electrical Engineering and Communication Brno University of Technology Brno Czechia

Department of Mathematical Analysis and Applications of Mathematics Faculty of Science Palacký University Olomouc Olomouc Czech Republic

Department of Medical Biochemistry Oslo University Hospital Oslo Norway

Department of Molecular and Clinical Pathology and Medical Genetics University Hospital Ostrava Ostrava Czechia

Department of Oncology KU Leuven Leuven Flanders Belgium

Institute of Experimental Endocrinology Biomedical Research Center Slovak Academy of Sciences Bratislava Slovakia

Institute of Neuroimmunology Slovak Academy of Sciences Bratislava Slovakia

Laboratory for Inherited Metabolic Disorders Department of Clinical Biochemistry University Hospital Olomouc and Faculty of Medicine and Dentistry Palacký University Olomouc Olomouc Czechia

Laboratory of Applied Mass Spectrometry Department of Cellular and Molecular Medicine KU Leuven Leuven Flanders Belgium

Laboratory of Integrative Cancer Genomics VIB KU Leuven Center for Cancer Biology Leuven Flanders Belgium

Laboratory of Lipid Metabolism and Cancer Department of Oncology Leuven Cancer Institute KU Leuven Leuven Flanders Belgium

Laboratory of Multi Omic Integrative Bioinformatics Department of Human Genetics KU Leuven Leuven Flanders Belgium

Metabolomics Core Facility VIB KU Leuven Center for Cancer Biology Leuven Flanders Belgium

Molecular Systems Biology Department of Functional and Evolutionary Ecology Faculty of Life Sciences University of Vienna Vienna Austria

South Australian Health and Medical Research Institute North Terrace Adelaide SA Australia

South Australian immunoGENomics Cancer Institute and Freemasons Centre for Male Health and Well Being The University of Adelaide Medical School North Terrace Adelaide SA Australia

VIB Center for AI and Computational Biology Leuven Flanders Belgium

Vienna Metabolomics Center University of Vienna Vienna Austria

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