> For the complete documentation index, see [llms.txt](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/introduction/from-authors.md). # From Authors

Cover design and preparation - Bogna Idkowiak.

**Welcome!** Welcome to the first version of *Omics Data Visualization in R and Python*! This GitBook is designed to be your go-to resource for mastering data visualization, statistical computations, and best practices in R and Python, with a focus on **lipidomics and metabolomics datasets**. Our goal is simple: to bring together the most effective **code snippets, visualizations, and computational approaches**—all presented in a clear and accessible way. R and Python have become essential tools for **omics data analysis**, offering powerful, free-of-charge solutions for generating high-quality visual insights and conducting complex statistical analyses. We believe that **learning these tools should be accessible to everyone**. That’s why we created this GitBook—a comprehensive collection of everything a young lipidomics or metabolomics researcher needs to **analyze bulk omics data** efficiently. Let’s dive in and explore the world of **omics data visualization** together! 🚀 The authors #### **Getting Started with R and Python** **For Beginners:** If you're just starting your journey with R or Python, we recommend following these steps:\ 1️⃣ Before modifying the code for your own data, first **work through the examples in this GitBook** using the dataset we’ve provided.\ 2️⃣ **Reproduce the visualizations on your computer** and ensure you understand each step of the code.\ 3️⃣ Once you're comfortable with the process, **start adapting the code snippets to your own data**. You can download the general dataset from **Introduction: Example Data Sets** (always start with dataset no. 1). If a different dataset is used in a specific chapter, we’ll always provide the source. **For Those with Some Experience:** If you already have a basic understanding of R and Python but want to test specific code snippets, you can download the example dataset from **Introduction: Example Data Sets** (dataset no. 1). Happy coding! 🚀 **Spotted an Issue? Here’s How to Report It** Dear GitBook reader, if you encounter any inconsistencies or errors in the R or Python code, please let us know at ****. Please use the example **data set no. 1** (from Introduction: Example data sets) to present why the code does not work. Is your favorite R or Python library missing? Let us know if you think it should be included! We will gladly update the repository so everyone can learn R and Python freely! Last update of the GitBook: 20.03.2025 #### **Authors and Affiliations** **Jakub Idkowiak** * University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Czech Republic; * Laboratory of Lipid Metabolism and Cancer, KU Leuven and Leuven Cancer Institute (LKI), Belgium.
**Jonas Dehairs** * Laboratory of Lipid Metabolism and Cancer, KU Leuven and Leuven Cancer Institute (LKI), Belgium.
**Jana Schwarzerová** * Brno University of Technology, Faculty of Electrical Engineering and Communication, Department of Biomedical Engineering, Czech Republic; * Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Austria; * Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Czech Republic.
**Dominika Olešová** * Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Slovakia; * Institute of Neuroimmunology, Slovak Academy of Sciences, Slovakia.
**Jacob X.M. Truong** * South Australian Health and Medical Research Institute (SAHMRI), Australia; * South Australian immunoGENomics Cancer Institute (SAiGENCI) & Freemasons Centre for Male Health and Well-Being, The University of Adelaide Medical School, Australia.
**Aleš Kvasnička** * Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University, Czech Republic; * Department of Medical Biochemistry, Oslo University Hospital, Norway.
**Marios Eftychiou** * Laboratory for Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Belgium; * VIB Center for AI & Computational Biology, Belgium; * Department of Oncology, KU Leuven, Belgium; * Laboratory of Multi-Omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Belgium.
**Ruben Cools** * Laboratory for Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Belgium; * VIB Center for AI & Computational Biology, Belgium; * Department of Oncology, KU Leuven, Belgium.
**Xander Spotbeen** * Laboratory of Lipid Metabolism and Cancer, KU Leuven and Leuven Cancer Institute (LKI), Belgium.
**Robert Jirásko** * University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Czech Republic.
**Vullnet Veseli** * University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Czech Republic.
**Marco Giampà** * Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Belgium; * Metabolomics Core Facility, VIB KU Leuven Center for Cancer Biology, Belgium.
**Vincent de Laat** * Laboratory of Lipid Metabolism and Cancer, KU Leuven and Leuven Cancer Institute (LKI), Belgium.
**Lisa M. Butler** * South Australian Health and Medical Research Institute (SAHMRI), Australia; * South Australian immunoGENomics Cancer Institute (SAiGENCI) & Freemasons Centre for Male Health and Well-Being, The University of Adelaide Medical School, Australia.
**Wolfram Weckwerth** * Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Austria; * Vienna Metabolomics Center (VIME), University of Vienna, Austria.
**David Friedecký** * Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University, Czech Republic.
**Jonas Demeulemeester** * Laboratory for Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Belgium; * VIB Center for AI & Computational Biology, Belgium; * Department of Oncology, KU Leuven, Belgium.
**Karel Hron** * Palacký University Olomouc, Faculty of Science, Department of Mathematical Analysis and Applications of Mathematics, Czech Republic.
**Johannes V. Swinnen** * Laboratory of Lipid Metabolism and Cancer, KU Leuven and Leuven Cancer Institute (LKI), Belgium.
**Project supervision:** **Michal Holčapek** * University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Czech Republic.