Hello, I would like to commend you on the development of MMuphin. It has been an invaluable tool for our meta-analysis of microbial communities.
I noticed that the current version of MMuphin uses Maaslin2 for its lm_meta function to correct for batch effects and perform group-wise differential analysis. Specifically, the function runs Maaslin2 models on the exposure with optional covariates/random covariates in each batch. Recently, Maaslin3 was released with significant improvements, including the ability to summarize both prevalence and abundance for differential analysis. This new feature provides a more comprehensive understanding of microbial associations in complex datasets.
Given the advancements in Maaslin3, I am wondering if there are any plans to update MMuphin to integrate Maaslin3 instead of Maaslin2. This would enhance the functionality of MMuphin and allow researchers to leverage the latest improvements in microbial association analysis.
Thank you for considering this request.