9.1 Analyzing 16S rRNA Data with phyloseq

In this section we will do more advanced analyses in phyloseq. These include:

1. Profiling biodiveristy of sample through alpha diversity
2. Plotting samples in a multidimensional plot which will allow us to easily see similarities between samples
3. Performing a differential abundance analysis to compare the abundance of microbes between two conditions
4. Relating all the above to different metadata variables in our datasets such as subject, age, and gender

These analyses are slightly more complex to run and interpret, but students who have completed the chapter on scientific literature will have previous exposure to these figures.

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