{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T04:08:12Z","timestamp":1754021292613,"version":"3.41.2"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T00:00:00Z","timestamp":1721865600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Most tools for normalizing NanoString gene expression data, apart from the default NanoString nCounter software, are R packages that focus on technical normalization and lack configurable parameters. However, content normalization is the most sensitive, experiment-specific, and relevant step to preprocess NanoString data. Currently this step requires the use of multiple tools and a deep understanding of data management by the researcher. We present GUANIN, a comprehensive normalization tool that integrates both new and well-established methods, offering a wide variety of options to introduce, filter, choose, and evaluate reference genes for content normalization. GUANIN allows the introduction of genes from an endogenous subset as reference genes, addressing housekeeping-related selection problems. It performs a specific and straightforward normalization approach for each experiment, using a wide variety of parameters with suggested default values. GUANIN provides a large number of informative output files that enable the iterative refinement of the normalization process. In terms of normalization, GUANIN matches or outperforms other available methods. Importantly, it allows researchers to interact comprehensively with the data preprocessing step without programming knowledge, thanks to its easy-to-use Graphical User Interface (GUI).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GUANIN can be installed with pip install GUANIN and it is available at https:\/\/pypi.org\/project\/guanin\/. Source code, documentation, and case studies are available at https:\/\/github.com\/julimontoto\/guanin under the GPLv3 license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae462","type":"journal-article","created":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T12:14:19Z","timestamp":1721909659000},"source":"Crossref","is-referenced-by-count":1,"title":["GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization"],"prefix":"10.1093","volume":"40","author":[{"given":"Juli\u00e1n","family":"Montoto-Louzao","sequence":"first","affiliation":[{"name":"Unidade de Xen\u00e9tica, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Gen\u00e9tica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigaci\u00f3n Sanitaria (IDIS), Hospital Cl\u00ednico Universitario de Santiago (SERGAS), 15706 , Santiago de Compostela, Spain"},{"name":"Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigaci\u00f3n Sanitaria de Santiago, Santigo de Compostela, 15706, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Respiratorias (CIBER-ES) , Madrid, 28029, Spain"}]},{"given":"Alberto","family":"G\u00f3mez-Carballa","sequence":"additional","affiliation":[{"name":"Unidade de Xen\u00e9tica, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Gen\u00e9tica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigaci\u00f3n Sanitaria (IDIS), Hospital Cl\u00ednico Universitario de Santiago (SERGAS), 15706 , Santiago de Compostela, Spain"},{"name":"Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigaci\u00f3n Sanitaria de Santiago, Santigo de Compostela, 15706, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Respiratorias (CIBER-ES) , Madrid, 28029, 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Group, Instituto de Investigaci\u00f3n Sanitaria (IDIS), Hospital Cl\u00ednico Universitario de Santiago (SERGAS), 15706 , Santiago de Compostela, Spain"},{"name":"Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigaci\u00f3n Sanitaria de Santiago, Santigo de Compostela, 15706, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Respiratorias (CIBER-ES) , Madrid, 28029, Spain"}]},{"given":"Alba","family":"Camino-Mera","sequence":"additional","affiliation":[{"name":"Unidade de Xen\u00e9tica, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Gen\u00e9tica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigaci\u00f3n Sanitaria (IDIS), Hospital Cl\u00ednico Universitario de Santiago (SERGAS), 15706 , Santiago de Compostela, Spain"},{"name":"Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigaci\u00f3n Sanitaria de Santiago, Santigo de Compostela, 15706, Spain"}]},{"given":"Sandra","family":"Viz-Lasheras","sequence":"additional","affiliation":[{"name":"Unidade de Xen\u00e9tica, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Gen\u00e9tica de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigaci\u00f3n Sanitaria (IDIS), Hospital Cl\u00ednico Universitario de Santiago (SERGAS), 15706 , Santiago de Compostela, Spain"},{"name":"Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigaci\u00f3n Sanitaria de Santiago, Santigo de Compostela, 15706, Spain"}]},{"given":"Mar\u00eda J","family":"Mart\u00edn","sequence":"additional","affiliation":[{"name":"CITIC, Computer Architecture Group, Universidade da Coru\u00f1a, Facultad de Inform\u00e1tica , 15071, A Coru\u00f1a, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9023-581X","authenticated-orcid":false,"given":"Federico","family":"Martin\u00f3n-Torres","sequence":"additional","affiliation":[{"name":"Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigaci\u00f3n Sanitaria de Santiago, Santigo de Compostela, 15706, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Respiratorias (CIBER-ES) , Madrid, 28029, Spain"},{"name":"Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Cl\u00ednico Universitario de Santiago de Compostela , Santiago de Compostela, Choupana s\/n, Santiago de Compostela, 15706, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2336-702X","authenticated-orcid":false,"given":"Antonio","family":"Salas","sequence":"additional","affiliation":[{"name":"Unidade de Xen\u00e9tica, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Gen\u00e9tica de 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