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

Abstract

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).This work has been funded by the STATegra project, EU FP7 grant number 30600 and the Spanish MINECO grant BIO2012-40244