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RUCova removes unwanted covariance from measured markers applying multivariate linear regression based on surrogates of sources of unwanted covariance (SUCs) and principal component analysis (PCA). We exemplify the use of RUCova and show that it effectively removes unwanted covariance while preserving genuine biological signals. Our results demonstrate the efficacy of RUCova in elucidating complex data patterns, facilitating the identification of activated signalling pathways, and improving the classification of important cell populations such as apoptotic cells. By providing a robust framework for data normalization and interpretation, RUCova enhances the accuracy and reliability of mass cytometry analyses, contributing to advances in our understanding of cellular biology and disease mechanisms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The R package is available on https:\/\/github.com\/molsysbio\/RUCova. Detailed documentation, data, and the code required to reproduce the results are available on https:\/\/doi.org\/10.5281\/zenodo.10913464.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae669","type":"journal-article","created":{"date-parts":[[2024,11,11]],"date-time":"2024-11-11T07:19:18Z","timestamp":1731309558000},"source":"Crossref","is-referenced-by-count":1,"title":["RUCova: Removal of Unwanted Covariance in mass cytometry data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1179-4080","authenticated-orcid":false,"given":"Rosario","family":"Astaburuaga-Garc\u00eda","sequence":"first","affiliation":[{"name":"Institute of Pathology, Charit\u00e9-Universit\u00e4tsmedizin Berlin , Berlin, 10117,","place":["Germany"]},{"name":"Institute of Biology, Humboldt Universit\u00e4t zu Berlin , Berlin, 10117,","place":["Germany"]}]},{"given":"Thomas","family":"Sell","sequence":"additional","affiliation":[{"name":"Institute of 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10117,","place":["Germany"]}]},{"given":"Kirsten","family":"Lauber","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, University Hospital, LMU M\u00fcnchen , Munich, 81377,","place":["Germany"]},{"name":"German Cancer Consortium (DKTK) , Munich, 81377,","place":["Germany"]},{"name":"Clinical Cooperation Group \u2018Personalized Radiotherapy in Head and Neck Cancer\u2019 Helmholtz Center Munich, German Research Center for Environmental Health GmbH , Neuherberg, 85764,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0171-7447","authenticated-orcid":false,"given":"Nils","family":"Bl\u00fcthgen","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Charit\u00e9-Universit\u00e4tsmedizin Berlin , Berlin, 10117,","place":["Germany"]},{"name":"Institute of Biology, Humboldt Universit\u00e4t zu Berlin , Berlin, 10117,","place":["Germany"]},{"name":"German Cancer Consortium (DKTK) , Berlin, 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