Hi there!
I've been following the tutorial for doing analysis in R with qiime2 objects using the pretty classic tutorial https://forum.qiime2.org/t/tutorial-integrating-qiime2-and-r-for-data-visualization-and-analysis-using-qiime2r/4121
Towards the end it shows some plots for differential abundance, however it uses the q2-aldex plugin, which doesn't seem to work for modern versions of QIIME2. I've tried to install older versions of QIIME2 but it doesn't seem to work. I'm just thinking I would rather just do this with my ANCOM-BC output, but I'm not sure how to modify the code to make it work with the ANCOM-BC output, can anyone help?
TLDR: How do I make differential abundance analysis work in qiime2r with ANCOM-BC output instead of Aldex?