use a microarray-based R package with RNAseq data?

[piemmea]

Hi all
I need to analyze a time series experiment assayed by RNAseq. I was told that BETR is a good package for that, but it is built for analyzing microarrays... I'm a newbie in such things and I wonder whether there is a way to let BETR (or a similar package) work with my RNAseq data: any thoughts?
Thanks a lot!

[shi]

You can use limma for your analysis. After read mapping and summarization, you can run voom for normalization and then perform differential expression analysis. Limma users guide has case studies for analyzing RNA-seq data.