Tool/Packages for integrated DE expression analysis of Time course miRAN and mRNA ?

Question

[bioinforupesh2009.au]

Hello guys,

I need any tool or R bioconductor packages for integrated DE expression analysis of miRAN and mRNA of time course data.

I have time course (4 time points with replicates[unfortunate not equally replicates from one time point to another]) expression matrix (transformed and normalized).

Thanks