You can use R to solve the problem.
Install the phyloseq R package and import the data_phyloseq.rds into R. Then you can extract the abundance table and taxonomy table and export them as .csv file for the MicrobiomeAnalyst input.
Hope this helps and let me know if you have more questions.
I found another way to go around that, thank you ! Now I am just having an issue with the tool crashing and having to reinput everything at each time. Is there any way to save a session / parameters or input some of the R code we save ?
I’m not sure if I understand your question correctly. But if you mean you want save the parameter you have used on the website, you can simply download the R history. Our website cannot directly accept R session or script as input.
An alternative way is to install our R package. Then you can use the downloaded R command and save the working session for continuous work.