Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series
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Título: | Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series |
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Autor/es: | Nueda, María José | Tarazona, Sonia | Conesa, Ana |
Grupo/s de investigación o GITE: | Sistemas Dinámicos y Estadística (SISDINEST) |
Centro, Departamento o Servicio: | Universidad de Alicante. Departamento de Estadística e Investigación Operativa |
Palabras clave: | maSigPro | RNA-seq time series | Bioconductor package |
Área/s de conocimiento: | Estadística e Investigación Operativa |
Fecha de publicación: | 3-jun-2014 |
Editor: | Oxford University Press |
Cita bibliográfica: | Bioinformatics. 2014, Advance Access. doi:10.1093/bioinformatics/btu333 |
Resumen: | Motivation: The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time course experiments. maSigPro is an R package specifically suited for the analysis of time course gene expression data that was developed originally for microarrays and hence was limited in its application to count data. Results: We have updated maSigPro to support RNA-seq time series analysis by introducing Generalized Linear Models in the algorithm to support the modelling of count data while maintaining the traditional functionalities of the package. We show a good performance of the maSigPro-GLM method in several simulated time course scenarios and in a real experimental dataset. Availability: The package is freely available under the LGPL license from the Bioconductor web site (http://bioconductor.org). |
Patrocinador/es: | This work has been funded by the STATegra project, EU FP7 grant number 30600 and the Spanish MINECO grant BIO2012-40244. |
URI: | http://hdl.handle.net/10045/37965 |
ISSN: | 1367-4803 (Print) | 1460-2059 (Online) |
DOI: | 10.1093/bioinformatics/btu333 |
Idioma: | eng |
Tipo: | info:eu-repo/semantics/article |
Derechos: | © The Author(s) 2014. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, 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/bioinformatics/btu333 |
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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