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OSS-Lab / MetQy

Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)
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Manual curation of used KEGG database #4

Closed Juleny closed 3 years ago

Juleny commented 3 years ago

Dear Andreas, I would like to use your tool to analyse the metabolic potential of MAGs. I have tested it already and found out that a few modules are missing. Unfortunately, I do not have access to the KEGG ftp but I wonder if I could make manual modifications (adding modules) to the existing KEGG database file that is used in the package. Do you think that is possible?

Many thanks Julia

asmvernon commented 3 years ago

Hi Julia, Yes, that should be possible :)

I think you should be able to pull the data from https://github.com/OSS-Lab/MetQy/blob/master/MetQy_1.1.0/R/sysdata.rda, modify it to add the new modules, and pass it using the "use_module_reference_table" argument.

Hope that works!

Thanks, Andrea

Juleny commented 3 years ago

Thank you Andrea, that worked very well :).

Julia