SLiMEbook- 1 min
I published an IBD paper in PLoSONE - showing one of the first application of ML methods to microbiome data. We dubbed the code used for the analysis SLiME.
The SLiME code (written in R) became outdated pretty quickly. We decided that the code, as it was packaged for the publication of the paper, should not be in the open anymore.
In its place, this ipython notebook will serve as a repository of the analysis. I hope this can be the starting point for others trying to follow the same approach and improve upon it. It leverages python, sklearn and pandas.