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

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Title: Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data.
Authors: Idkowiak J; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia.; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium., Dehairs J; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium., Schwarzerová J; Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia.; Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.; Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia., Olešová D; Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia., Truong JXM; South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, SA, Australia.; South Australian immunoGENomics Cancer Institute (SAiGENCI) & Freemasons Centre for Male Health and Well-Being, The University of Adelaide Medical School, North Terrace, Adelaide, SA, Australia., Kvasnička A; Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia.; Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway., Eftychiou M; Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium.; VIB Center for AI & Computational Biology, Leuven, Flanders, Belgium.; Department of Oncology, KU Leuven, Leuven, Flanders, Belgium.; Laboratory of Multi-Omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Leuven, Flanders, Belgium., Cools R; Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium.; VIB Center for AI & Computational Biology, Leuven, Flanders, Belgium.; Department of Oncology, KU Leuven, Leuven, Flanders, Belgium., Spotbeen X; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium., Jirásko R; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia., Veseli V; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia., Giampà M; Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Flanders, Belgium.; Metabolomics Core Facility, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium., de Laat V; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium., Butler LM; South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, SA, Australia.; South Australian immunoGENomics Cancer Institute (SAiGENCI) & Freemasons Centre for Male Health and Well-Being, The University of Adelaide Medical School, North Terrace, Adelaide, SA, Australia., Weckwerth W; Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria., Friedecký D; Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia., Demeulemeester J; Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium.; VIB Center for AI & Computational Biology, Leuven, Flanders, Belgium.; Department of Oncology, KU Leuven, Leuven, Flanders, Belgium., Hron K; Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic., Swinnen JV; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium., Holčapek M; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia. Michal.Holcapek@upce.cz.
Source: Nature communications [Nat Commun] 2025 Sep 30; Vol. 16 (1), pp. 8714. Date of Electronic Publication: 2025 Sep 30.
Publication Type: Journal Article; Review
Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
Database: MEDLINE Ultimate
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  Data: Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data.
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  Data: <searchLink fieldCode="AU" term="%22Idkowiak+J%22">Idkowiak J</searchLink>; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia.; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Dehairs+J%22">Dehairs J</searchLink>; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Schwarzerová+J%22">Schwarzerová J</searchLink>; Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia.; Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.; Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia.<br /><searchLink fieldCode="AU" term="%22Olešová+D%22">Olešová D</searchLink>; Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.<br /><searchLink fieldCode="AU" term="%22Truong+JXM%22">Truong JXM</searchLink>; South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, SA, Australia.; South Australian immunoGENomics Cancer Institute (SAiGENCI) & Freemasons Centre for Male Health and Well-Being, The University of Adelaide Medical School, North Terrace, Adelaide, SA, Australia.<br /><searchLink fieldCode="AU" term="%22Kvasnička+A%22">Kvasnička A</searchLink>; Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia.; Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.<br /><searchLink fieldCode="AU" term="%22Eftychiou+M%22">Eftychiou M</searchLink>; Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium.; VIB Center for AI & Computational Biology, Leuven, Flanders, Belgium.; Department of Oncology, KU Leuven, Leuven, Flanders, Belgium.; Laboratory of Multi-Omic Integrative Bioinformatics, Department of Human Genetics, KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Cools+R%22">Cools R</searchLink>; Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium.; VIB Center for AI & Computational Biology, Leuven, Flanders, Belgium.; Department of Oncology, KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Spotbeen+X%22">Spotbeen X</searchLink>; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Jirásko+R%22">Jirásko R</searchLink>; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia.<br /><searchLink fieldCode="AU" term="%22Veseli+V%22">Veseli V</searchLink>; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia.<br /><searchLink fieldCode="AU" term="%22Giampà+M%22">Giampà M</searchLink>; Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Flanders, Belgium.; Metabolomics Core Facility, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22de+Laat+V%22">de Laat V</searchLink>; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Butler+LM%22">Butler LM</searchLink>; South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, SA, Australia.; South Australian immunoGENomics Cancer Institute (SAiGENCI) & Freemasons Centre for Male Health and Well-Being, The University of Adelaide Medical School, North Terrace, Adelaide, SA, Australia.<br /><searchLink fieldCode="AU" term="%22Weckwerth+W%22">Weckwerth W</searchLink>; Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.<br /><searchLink fieldCode="AU" term="%22Friedecký+D%22">Friedecký D</searchLink>; Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia.<br /><searchLink fieldCode="AU" term="%22Demeulemeester+J%22">Demeulemeester J</searchLink>; Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Flanders, Belgium.; VIB Center for AI & Computational Biology, Leuven, Flanders, Belgium.; Department of Oncology, KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Hron+K%22">Hron K</searchLink>; Department of Mathematical Analysis and Applications of Mathematics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.<br /><searchLink fieldCode="AU" term="%22Swinnen+JV%22">Swinnen JV</searchLink>; Laboratory of Lipid Metabolism and Cancer, Department of Oncology, Leuven Cancer Institute (LKI) and Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium.<br /><searchLink fieldCode="AU" term="%22Holčapek+M%22">Holčapek M</searchLink>; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czechia. Michal.Holcapek@upce.cz.
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