Which tool to use to find cycling genes

Question

[mr.udvr]

Dear all,

we have an experiment with 2 conditions (treated/untreated). For each we measure the expression level of genes (RNA-Seq) in six different time points, and for each time point we have 3 replicates. The major goal would be to find cycling genes. Which tool would you use for doing that and why? Is JTK Cycle, ARSER good for that or should I use DyNB? I read that also DESeq2 has an option for doing that. As I have no experience yet, any suggestion would be appreciated.

Thanks in advance!

Udi

Answer 1

[Jean-Karim Heriche]

What about the Bioconductor cycle package ? You may also want to have a look at this related biostar question.
You have few time points and most time series analysis methods typically rely on longer series. You could also do some clustering to see if you can spot any interesting pattern.

Answer 2

[mr.udvr]

Thank you Jean-Karim!

[Naren]

Good that you are grateful. Learn to write this in comments not as an answer.

[mr.udvr]

You are right, thanks :)