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

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.

Researchers at the University of Alicante 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. They show a good performance of the maSigPro-GLM method in several simulated time course scenarios and in a real experimental dataset.

rna-seq

 

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

CONTACT: mj.nueda@ua.es,  aconesa@cipf.es.

Nueda MJ, Tarazona S, Conesa A. (2014) Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series. Bioinformatics [Epub ahead of print]. [article]