I have readcount data from my metagenome experiment. My metagenome experiment looks like this:
control T0 T1 T2 T3 T4 case T0 T1 T2 T3 T4
I have two conditions (case and control) and five time points. I have readcounts data from each control and case samples across these 5 time points. I want to conduct analysis as below:
Calculate abundance differences within each condition i.e. control and for example, T0 vs T4, T1 vs T4, T2 vs T4 and T3 vs T4). Like which taxa is significantly different at different time point compared to baseline (T4).
Measure differences between control and cases on each time point i.e case vs control @ T0, case vs control @ T1, case vs control @ T2, case vs control @ T3, case vs control @ T4.
I know I should be doing time series analysis but I don't know how to perform this complex longitudinal analysis.
I would really appreciate if you someone could help me in deciding where to start? Or direct me to any tutorial where I could learn and apply the same on my data.