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Studying Biological Diveristy #105

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gregcaporaso opened this Issue Mar 30, 2015 · 0 comments

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gregcaporaso commented Mar 30, 2015

This chapter will be re-written to use QIIME 2 in Spring 2017 as part of my Microbiome Bioinformatics with QIIME 2 course at NAU.

  • replace static tree images with auto-generated tree images
  • replace all links to local images with links to GitHub hosted images
  • update ordination plots to use scikit-bio's built-in
  • add pick OTUs through OTU table section (work with the "tiny-test" or the q2d2 test data) (save this for the QIIME book)
  • add alpha rarefaction section
  • add Jaccard distance, weighted unifrac distance
  • add comparing alpha diversity section
  • add identifying significantly different OTUs section (including Waste Not, Want Not, group_significance.py methods, supervised_classification.py, ANCOM methods)
  • add exploring taxonomy section using code from DB search chapter.
  • replace t-tests with ANOSIM
  • add reference to GUSTAME
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