**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.
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