{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T06:02:45Z","timestamp":1768284165230,"version":"3.49.0"},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T00:00:00Z","timestamp":1707868800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T00:00:00Z","timestamp":1707868800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100004710","name":"Fondazione Umberto Veronesi","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004710","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002954","name":"Universit\u00e0 degli Studi di Milano-Bicocca","doi-asserted-by":"publisher","award":["Bicocca 2020 Starting Grant"],"award-info":[{"award-number":["Bicocca 2020 Starting Grant"]}],"id":[{"id":"10.13039\/501100002954","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021856","name":"Ministero dell'Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["Dipartimenti di Eccellenza 2023-2027 (l. 232\/2016, art. 1, commi 314 - 337)"],"award-info":[{"award-number":["Dipartimenti di Eccellenza 2023-2027 (l. 232\/2016, art. 1, commi 314 - 337)"]}],"id":[{"id":"10.13039\/501100021856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["AIRC Investigator Grant Ig 22082"],"award-info":[{"award-number":["AIRC Investigator Grant Ig 22082"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Copy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer progression by affecting gene expression and genomic stability. Computational techniques can analyze copy number data obtained from high-throughput sequencing platforms, and various tools visualize and analyze CNAs in cancer genomes, providing insights into genetic mechanisms driving cancer development and progression. However, tools for visualizing copy number data in cancer research have some limitations. In fact, they can be complex to use and require expertise in bioinformatics or computational biology. While copy number data analysis and visualization provide insights into cancer biology, interpreting results can be challenging, and there may be multiple explanations for observed patterns of copy number alterations.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We created Control-FREEC Viewer, a tool that facilitates effective visualization and exploration of copy number data. With Control-FREEC Viewer, experimental data can be easily loaded by the user. After choosing the reference genome, copy number data are displayed in whole genome or single chromosome view. Gain or loss on a specific gene can be found and visualized on each chromosome. Analysis parameters for subsequent sessions can be stored and images can be exported in raster and vector formats.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Control-FREEC Viewer enables users to import and visualize data analyzed by the Control-FREEC tool, as well as by other tools sharing a similar tabular output, providing a comprehensive and intuitive graphical user interface for data visualization.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-024-05694-w","type":"journal-article","created":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T15:03:09Z","timestamp":1707922989000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data"],"prefix":"10.1186","volume":"25","author":[{"given":"Valentina","family":"Crippa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emanuela","family":"Fina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniele","family":"Ramazzotti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rocco","family":"Piazza","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,2,14]]},"reference":[{"issue":"6","key":"5694_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gm62","volume":"1","author":"A Shlien","year":"2009","unstructured":"Shlien A, Malkin D. Copy number variations and cancer. Genome Med. 2009;1(6):1\u20139. https:\/\/doi.org\/10.1186\/gm62.","journal-title":"Genome Med"},{"issue":"10","key":"5694_CR2","doi-asserted-by":"publisher","first-page":"1134","DOI":"10.1038\/ng.2760","volume":"45","author":"TI Zack","year":"2013","unstructured":"Zack TI, Schumacher SE, Carter SL, et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013;45(10):1134\u201340. https:\/\/doi.org\/10.1038\/ng.2760.","journal-title":"Nat Genet"},{"issue":"11","key":"5694_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-14-S11-S1","volume":"14","author":"M Zhao","year":"2013","unstructured":"Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinform. 2013;14(11):1\u201316. https:\/\/doi.org\/10.1186\/1471-2105-14-S11-S1.","journal-title":"BMC Bioinform."},{"issue":"2","key":"5694_CR4","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","unstructured":"Thorvaldsd\u00f3ttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178\u201392. https:\/\/doi.org\/10.1093\/bib\/bbs017.","journal-title":"Brief Bioinform"},{"issue":"269","key":"5694_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1126\/scisignal.2004088","volume":"6","author":"J Gao","year":"2013","unstructured":"Gao J, Aksoy BA, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal complementary data sources and analysis options. Sci Signal. 2013;6(269):1\u201320. https:\/\/doi.org\/10.1126\/scisignal.2004088.","journal-title":"Sci Signal"},{"issue":"5","key":"5694_CR6","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","volume":"2","author":"E Cerami","year":"2012","unstructured":"Cerami E, Gao J, Dogrusoz U, et al. The cBio Cancer Genomics Portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401\u20134. https:\/\/doi.org\/10.1158\/2159-8290.CD-12-0095.","journal-title":"Cancer Discov"},{"issue":"6","key":"5694_CR7","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1101\/gr.229102","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996\u20131006. https:\/\/doi.org\/10.1101\/gr.229102.","journal-title":"Genome Res"},{"issue":"5","key":"5694_CR8","doi-asserted-by":"publisher","first-page":"btad290","DOI":"10.1093\/bioinformatics\/btad290","volume":"39","author":"M Macnee","year":"2023","unstructured":"Macnee M, P\u00e9rez-Palma E, Br\u00fcnger T, et al. CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online. Bioinformatics. 2023;39(5):btad290. https:\/\/doi.org\/10.1093\/bioinformatics\/btad290.","journal-title":"Bioinformatics"},{"issue":"12","key":"5694_CR9","doi-asserted-by":"publisher","first-page":"e0189334","DOI":"10.1371\/journal.pone.0189334","volume":"12","author":"V Renault","year":"2017","unstructured":"Renault V, Tost J, Pichon F, Wang-Renault SF, Letouz\u00e9 E, Imbeaud S, Zucman-Rossi J, Deleuze JF, How-Kit A. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations. PLoS One. 2017;12(12):e0189334. https:\/\/doi.org\/10.1371\/journal.pone.0189334.","journal-title":"PLoS One."},{"key":"5694_CR10","doi-asserted-by":"publisher","unstructured":"Collins RL, Stone MR, Brand H, Glessner JT, Talkowski ME. CNView: a visualization and annotation tool for copy number variation from whole-genome sequencing 2016. doi:https:\/\/doi.org\/10.1101\/049536","DOI":"10.1101\/049536"},{"issue":"3","key":"5694_CR11","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1093\/bioinformatics\/btr670","volume":"28","author":"V Boeva","year":"2012","unstructured":"Boeva V, Popova T, Bleakley K, et al. Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics. 2012;28(3):423\u20135. https:\/\/doi.org\/10.1093\/bioinformatics\/btr670.","journal-title":"Bioinformatics"},{"issue":"9","key":"5694_CR12","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.3324\/haematol.2017.179937","volume":"104","author":"V Magistroni","year":"2019","unstructured":"Magistroni V, Mauri M, D\u2019Aliberti D, et al. De novo UBE2A mutations are recurrently acquired during chronic myeloid leukemia progression and interfere with myeloid differentiation pathways. Haematologica. 2019;104(9):1789\u201397. https:\/\/doi.org\/10.3324\/haematol.2017.179937.","journal-title":"Haematologica"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05694-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-024-05694-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05694-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T15:03:13Z","timestamp":1707922993000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-024-05694-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,14]]},"references-count":12,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["5694"],"URL":"https:\/\/doi.org\/10.1186\/s12859-024-05694-w","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,14]]},"assertion":[{"value":"26 July 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 February 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 February 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"72"}}