I have been downloading the NCBI SRA fastq files and the project has the same patients sampled at multiple time points during the treatment. Could you please suggest how I can do the analysis for longitudinal time-series microbiome data in microbiomeanalyst? I could not find the related post in the forum and if I have missed it, please could you direct me to the tutorial or post?
Look at the ‘Multi-factor analysis’ tool inside the “Comparisons & Classifications” module. Multiple regression is very flexible - you can include ‘patient ID’ as either a covariate or a blockign factor (depending if you want to model it as fixed or random effects) to account for repeated measures, and specify ‘time’ as your primary metadata if you want to find microbial features associated with time.
The tool provides an interface for standard mixed effect models, so you can try learn more about this topic in general if you are having trouble specifying your model.
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