Journal
BIOINFORMATICS
Volume 30, Issue 18, Pages 2598-2602Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu333
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Funding
- FP7 STATegra project [GA-30600]
- EU FP7 [30600]
- Spanish MINECO [BIO2012-40244]
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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.
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