Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
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Título: | Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package |
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Autor/es: | Tarazona, Sonia | Furió-Tarí, Pedro | Turrà, David | Di Pietro, Antonio | Nueda, María José | Ferrer, Alberto | Conesa, Ana |
Grupo/s de investigación o GITE: | Sistemas Dinámicos y Estadística (SISDINEST) |
Centro, Departamento o Servicio: | Universidad de Alicante. Departamento de Matemáticas |
Palabras clave: | RNA-seq | NOISeq R/Bioc package | Data quality | Differential expression |
Área/s de conocimiento: | Estadística e Investigación Operativa |
Fecha de publicación: | 2-dic-2015 |
Editor: | Oxford University Press |
Cita bibliográfica: | Nucleic Acids Research. 2015, 43(21): e140. doi:10.1093/nar/gkv711 |
Resumen: | As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression. |
Patrocinador/es: | European Union Seventh Framework Programme [FP7/2007-2013, 306000]; Spanish Ministry of Science and Innovation [MICINN, BIO2008-04638-E], in the framework of ERA-Net Pathogenomics; MICINN [DPI2008-06880-C03-03/DPI]. Funding for open access charge: University of Florida, Publication Funds. |
URI: | http://hdl.handle.net/10045/51805 |
ISSN: | 0305-1048 (Print) | 1362-4962 (Online) |
DOI: | 10.1093/nar/gkv711 |
Idioma: | eng |
Tipo: | info:eu-repo/semantics/article |
Derechos: | © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. |
Revisión científica: | si |
Versión del editor: | http://dx.doi.org/10.1093/nar/gkv711 |
Aparece en las colecciones: | INV - SISDINEST - Artículos de Revistas Investigaciones financiadas por la UE INV - AppBiochem - Artículos de Revistas INV - GESTA - Artículos de Revistas |
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