{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T22:45:46Z","timestamp":1783723546838,"version":"3.55.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,2,20]],"date-time":"2024-02-20T00:00:00Z","timestamp":1708387200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004281","name":"National Science Centre","doi-asserted-by":"publisher","award":["2021\/43\/O\/ST6\/02805"],"award-info":[{"award-number":["2021\/43\/O\/ST6\/02805"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005297","name":"Medical University of Bia\u0142ystok","doi-asserted-by":"crossref","award":["B.SUB.23.53"],"award-info":[{"award-number":["B.SUB.23.53"]}],"id":[{"id":"10.13039\/501100005297","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Missing values are commonly observed in metabolomics data from mass spectrometry. Imputing them is crucial because it assures data completeness, increases the statistical power of analyses, prevents inaccurate results, and improves the quality of exploratory analysis, statistical modeling, and machine learning. Numerous Missing Value Imputation Algorithms (MVIAs) employ heuristics or statistical models to replace missing information with estimates. In the context of metabolomics data, we identified 52 MVIAs implemented across 70 R functions. Nevertheless, the usage of those 52 established methods poses challenges due to package dependency issues, lack of documentation, and their instability.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our R package, \u2018imputomics\u2019, provides a convenient wrapper around 41 (plus random imputation as a baseline model) out of 52 MVIAs in the form of a command-line tool and a web application. In addition, we propose a novel functionality for selecting MVIAs recommended for metabolomics data with the best performance or execution time.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>\u2018imputomics\u2019 is freely available as an R package (github.com\/BioGenies\/imputomics) and a Shiny web application (biogenies.info\/imputomics-ws). The documentation is available at biogenies.info\/imputomics.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae098","type":"journal-article","created":{"date-parts":[[2024,2,19]],"date-time":"2024-02-19T14:19:38Z","timestamp":1708352378000},"source":"Crossref","is-referenced-by-count":13,"title":["imputomics: web server and R package for missing values imputation in metabolomics data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5467-018X","authenticated-orcid":false,"given":"Jaros\u0142aw","family":"Chilimoniuk","sequence":"first","affiliation":[{"name":"Clinical Research Centre, Medical University of Bia\u0142ystok , Bia\u0142ystok, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2581-7722","authenticated-orcid":false,"given":"Krystyna","family":"Grzesiak","sequence":"additional","affiliation":[{"name":"Clinical Research Centre, Medical University of Bia\u0142ystok , Bia\u0142ystok, Poland"},{"name":"Faculty of Mathematics and Computer Science, University of Wroc\u0142aw , Wroc\u0142aw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7187-6988","authenticated-orcid":false,"given":"Jakub","family":"Ka\u0142a","sequence":"additional","affiliation":[{"name":"Clinical Research Centre, Medical University of Bia\u0142ystok , Bia\u0142ystok, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3515-4320","authenticated-orcid":false,"given":"Dominik","family":"Nowakowski","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Medical Informatics, Medical University of Bia\u0142ystok , Bia\u0142ystok, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4522-4978","authenticated-orcid":false,"given":"Adam","family":"Kr\u0119towski","sequence":"additional","affiliation":[{"name":"Clinical Research Centre, Medical University of Bia\u0142ystok , Bia\u0142ystok, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8145-579X","authenticated-orcid":false,"given":"Rafa\u0142","family":"Kolenda","sequence":"additional","affiliation":[{"name":"Quadram Institute Biosciences, Norwich Research Park , Norwich, United Kingdom"},{"name":"Faculty of Veterinary Medicine, Wroc\u0142aw University of Environmental and Life Sciences , Wroc\u0142aw, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3729-0518","authenticated-orcid":false,"given":"Micha\u0142","family":"Ciborowski","sequence":"additional","affiliation":[{"name":"Clinical Research Centre, 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