{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T18:53:56Z","timestamp":1767380036747,"version":"3.48.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T00:00:00Z","timestamp":1766016000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["UI\/BD\/153051\/2022"],"award-info":[{"award-number":["UI\/BD\/153051\/2022"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>High-throughput omics technologies generate complex datasets with thousands of features that are quantified across multiple experimental conditions, but often suffer from incomplete measurements, missing values, and individually fluctuating variances. This requires analytical tools for accurate, deep and insightful biological interpretation, capable of dealing with a large variety of data properties and different amounts of completeness. Software capable of handling such data complexity and integrating with external applications for downstream analysis remains rare and mostly relies on programming-based environments, limiting accessibility for researchers without computational expertise.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present OmicsQ, an interactive, web-based platform designed to streamline quantitative omics data analysis. OmicsQ provides an intuitive, browser-based visualization interface that integrates established statistical processing tools. Those include robust batch correction, automated experimental design annotation, and handling of missing data without imputation, which maintains data integrity and avoids artifacts from a priori assumptions. OmicsQ seamlessly interacts with external applications (e.g. PolySTest, VSClust, ComplexBrowser) for statistical testing, clustering, analysis of protein complex behavior, and pathway enrichment, offering a comprehensive and flexible workflow from data import to biological interpretation that is broadly applicable across domains.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>OmicsQ is implemented in R and Shiny and is available at https:\/\/computproteomics.bmb.sdu.dk\/app_direct\/OmicsQ. Source code and installation instructions: https:\/\/github.com\/computproteomics\/OmicsQ, DOI: 10.5281\/zenodo.17778420.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf660","type":"journal-article","created":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T12:51:54Z","timestamp":1765284714000},"source":"Crossref","is-referenced-by-count":0,"title":["OmicsQ: a user-friendly platform for interactive quantitative omics data analysis"],"prefix":"10.1093","volume":"42","author":[{"given":"Xuan-Tung","family":"Trinh","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense,","place":["Denmark"]}]},{"given":"Andr\u00e9","family":"Abrantes da Costa","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense,","place":["Denmark"]},{"name":"BioISI \u2013 Instituto de Biosistemas e Ci\u00eancias Integrativas, Faculdade de Ci\u00eancias da Universidade de Lisboa , 1749-016 Lisbon,","place":["Portugal"]}]},{"given":"David","family":"Bouyssi\u00e9","sequence":"additional","affiliation":[{"name":"Infrastructure Nationale de Prot\u00e9omique, ProFI , UAR 2048 Toulouse,","place":["France"]},{"name":"Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, Universit\u00e9 de Toulouse (UT) , 31077 Toulouse,","place":["France"]}]},{"given":"Adelina","family":"Rogowska-Wrzesinska","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 Odense,","place":["Denmark"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9708-6722","authenticated-orcid":false,"given":"Veit","family":"Schw\u00e4mmle","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , 5230 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