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

Bioinformatics
María José NuedaAna Conesa

Abstract

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. 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. The package is freely available under the LGPL license from the Bioconductor Web site (http://bioconductor.org).

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Related Concepts

Sequence Determinations, RNA
Log-Linear Models
Gene Expression
Computer Programs and Programming
Sequencing
Silo (Dataset)
MRNA Differential Display
Computational Molecular Biology

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