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Despite a rapid increase in the number of large-scale metabolomic studies, the analysis of metabolomic data remains a key challenge. Specifically, diverse unwanted variations and batch effects in processing many samples have a substantial impact on identifying true biological markers, and it is a daunting challenge to annotate a plethora of peaks as metabolites in untargeted mass spectrometry-based metabolomics. Therefore, the development of an out-of-the-box tool is urgently needed to realize data integration and to accurately annotate metabolites with enhanced functions. In this study, the LargeMetabo package based on R code was developed for processing and analyzing large-scale metabolomic data. This package is unique because it is capable of (1) integrating multiple analytical experiments to effectively boost the power of statistical analysis; (2) selecting the appropriate biomarker identification method by intelligent assessment for large-scale metabolic data and (3) providing metabolite annotation and enrichment analysis based on an enhanced metabolite database. The LargeMetabo package can facilitate flexibility and reproducibility in large-scale metabolomics. The package is freely available from https:\/\/github.com\/LargeMetabo\/LargeMetabo.<\/jats:p>","DOI":"10.1093\/bib\/bbac455","type":"journal-article","created":{"date-parts":[[2022,10,24]],"date-time":"2022-10-24T05:58:09Z","timestamp":1666591089000},"source":"Crossref","is-referenced-by-count":38,"title":["LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data"],"prefix":"10.1093","volume":"23","author":[{"given":"Qingxia","family":"Yang","sequence":"first","affiliation":[{"name":"Nanjing University of Posts and Telecommunications Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, , Nanjing, 210023 , China"},{"name":"Zhejiang University College of Pharmaceutical Sciences, , Hangzhou, Zhejiang 310058 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9944-0003","authenticated-orcid":false,"given":"Bo","family":"Li","sequence":"additional","affiliation":[{"name":"Chongqing Normal University, Chongqing College of Life Sciences, , Chongqing 401331 , China"}]},{"given":"Panpan","family":"Wang","sequence":"additional","affiliation":[{"name":"Huanghuai University College of Chemistry and Pharmaceutical Engineering, , Zhumadian 463000 , China"}]},{"given":"Jicheng","family":"Xie","sequence":"additional","affiliation":[{"name":"Nanjing University of Posts and Telecommunications Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, , Nanjing, 210023 , China"}]},{"given":"Yuhao","family":"Feng","sequence":"additional","affiliation":[{"name":"Nanjing University of Posts and Telecommunications Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, , Nanjing, 210023 , China"}]},{"given":"Ziqiang","family":"Liu","sequence":"additional","affiliation":[{"name":"Nanjing University of Posts and Telecommunications Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, , Nanjing, 210023 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8069-0053","authenticated-orcid":false,"given":"Feng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Zhejiang University College of Pharmaceutical Sciences, , Hangzhou, Zhejiang 310058 , China"}]}],"member":"286","published-online":{"date-parts":[[2022,10,21]]},"reference":[{"key":"2022112111194143400_ref1","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/s41586-021-03707-9","article-title":"A metabolomics pipeline for the mechanistic interrogation of the gut 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