Importing phyloseq.rds data

MicrobiomeAnalyst
1

Hello everyone,

Our collaborators that perform the sequencing part for our work provided us with a data_phyloseq.Rds object file and .tsv metadata.

If there any way to reverse back to the .biom abundance profile or any other format that would be suitable to be used in MicrobiomeAnalyst ?

Thank you and have a great day,

2

Hello,
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.

Best,
Yao

3

I think this can work indeed though I never used R, more of a python guy.

Will check it out,

Thank you Yao,

4

There might be a solution in python. You can try:

import pyreadr

result = pyreadr.read_r('/path/to/file.Rds')

Hope this works!

5

Hello,

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 ?

Thank you again,

6

Hello,

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.

Hope this helps.
Yao