GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization.

Autor:	Montoto-Louzao J; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Genética de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Spain.; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain.; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, 28029, Spain., Gómez-Carballa A; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Genética de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Spain.; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain.; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, 28029, Spain., Bello X; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Genética de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Spain.; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain.; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, 28029, Spain., Pardo-Seco J; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Genética de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Spain.; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain.; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, 28029, Spain., Camino-Mera A; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Genética de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Spain.; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain., Viz-Lasheras S; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Genética de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Spain.; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain., Martín MJ; CITIC, Computer Architecture Group, Universidade da Coruña, Facultad de Informática, 15071, A Coruña, Spain., Martinón-Torres F; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain.; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, 28029, Spain.; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Choupana s/n, Santiago de Compostela, 15706, Spain., Salas A; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and Genética de Poblaciones en Biomedicina (GenPoB) Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706, Santiago de Compostela, Spain.; Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santigo de Compostela, 15706, Spain.; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, 28029, Spain.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Aug 02; Vol. 40 (8).
DOI:	10.1093/bioinformatics/btae462
Abstrakt:	Summary: 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). Availability and Implementation: 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. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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