Susan Holmes
2017-07-27
Phyloseq API
(McMurdie and Holmes, 2013, Plos ONE).
phyloseq-measures-ggplot2
All standard ordinations.
Wolfgang Huber
The way the authors proceed is to follow the rarefying path
, this is not recommended and a much better procedure is to use DESeq with phyloseq, see the wiki here:
phyloseq-testing-deseq
phyloseq-networks
Package: phyloseqGraphTest
Using the tree
Taking account of the phylogenetic tree when testing:
Perturbation Design
Markov Model
Example Sankey
Example Treebox (Kris Sankaran)
Tutorial to follow (Kris Sankaran)
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