[BioC] time course analyses Illumina RNA-seq data

[Sandra Rehan]

I am looking for software to analyze time course data for an Illumina
gene expression data set (four lanes of paired end reads). I have two
biological replicates for seven time points. All packages that I am
aware of (bats, time course, edge) are designed for microarray data
analysis. Does someone know of a software package designed for
Illumina time course data?