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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.
Availability And Implementation: The package is freely available under the LGPL license from the Bioconductor Web site (http://bioconductor.org).
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155246 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btu333 | DOI Listing |
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