Hi. I have pathways result from Humann3 that I would like to perform stat and visualization. I have one metadata with categorical variables. Can I use LEfSe for this? Or should I go with Maaslin? Please provide your feedback. Thanks
Generally, we suggest migrating to MaAsLin at this point. We are still actively maintaining this tool, while LEfSe has not been under active support for several years.
The MaAsLin tutorial has a section that directly addresses using MaAsLin on the output of functional tools if you would like more information.