Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
Bioinformatics, 2014•academic.oup.com
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 …
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 …
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, 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 ).
Contact: mj.nueda@ua.es or aconesa@cipf.es
Oxford University Press