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Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series

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Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series

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dc.contributor.author Nueda, María José es_ES
dc.contributor.author Tarazona Campos, Sonia es_ES
dc.contributor.author Conesa, Ana es_ES
dc.date.accessioned 2016-05-02T12:49:37Z
dc.date.available 2016-05-02T12:49:37Z
dc.date.issued 2014-09-15
dc.identifier.issn 1367-4803
dc.identifier.uri http://hdl.handle.net/10251/63346
dc.description.abstract [EN] 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, which 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 modeling 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 and implementation: The package is freely available under the LGPL license from the Bioconductor Web site (http:// bioconductor.org) es_ES
dc.description.sponsorship This work has been funded by the FP7 STATegra [GA-30600] project, EU FP7 [30600] and the Spanish MINECO [BIO2012-40244]. en_EN
dc.language Inglés es_ES
dc.publisher Oxford University Press (OUP): Policy B - Oxford Open Option B es_ES
dc.relation.ispartof Bioinformatics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Differential expression analysis es_ES
dc.subject Gene es_ES
dc.subject Depth es_ES
dc.subject Course microarray experiments es_ES
dc.subject Normalization es_ES
dc.subject Sequence es_ES
dc.subject.classification ESTADISTICA E INVESTIGACION OPERATIVA es_ES
dc.title Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1093/bioinformatics/btu333
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//BIO2012-40244/ES/DESARROLLO DE RECURSOS COMPUTACIONALES PARA LA CARACTERIZACION Y ANOTACION FUNCIONAL DE ARN NO CODIFICANTE./ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/30600/EU/
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Estadística e Investigación Operativa Aplicadas y Calidad - Departament d'Estadística i Investigació Operativa Aplicades i Qualitat es_ES
dc.description.bibliographicCitation Nueda, MJ.; Tarazona Campos, S.; Conesa, A. (2014). Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series. Bioinformatics. 30(18):2598-2602. https://doi.org/10.1093/bioinformatics/btu333 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://dx.doi.org/10.1093/bioinformatics/btu333 es_ES
dc.description.upvformatpinicio 2598 es_ES
dc.description.upvformatpfin 2602 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 30 es_ES
dc.description.issue 18 es_ES
dc.relation.senia 269164 es_ES
dc.identifier.eissn 1460-2059
dc.identifier.pmid 24894503 en_EN
dc.identifier.pmcid PMC4155246 en_EN
dc.contributor.funder European Commission
dc.contributor.funder Ministerio de Economía y Competitividad
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