GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization
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http://hdl.handle.net/2183/38913Collections
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GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalizationAuthor(s)
Date
2024-08Citation
Julián Montoto-Louzao, Alberto Gómez-Carballa, Xabier Bello, Jacobo Pardo-Seco, Alba Camino-Mera, Sandra Viz-Lasheras, María J Martín, Federico Martinón-Torres, Antonio Salas, GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization, Bioinformatics, Volume 40, Issue 8, August 2024, btae462, https://doi.org/10.1093/bioinformatics/btae462
Abstract
[Abstract]: 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).
Keywords
NanoString
GUANIN
Gene Expression Profiling
Humans
Software
User-Computer Interface
GUANIN
Gene Expression Profiling
Humans
Software
User-Computer Interface
Description
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.
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Atribución 3.0 España