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# System prepended metadata

title: 'Compositional microbiome analysis in QIIME2 and related tools (March 30-31, 2021)'

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# Compositional microbiome analysis in QIIME2 and related tools (March 30-31, 2021)

Q&A + Discussion
* Panelists are here to facilitate any discussion / answer any questions



Workshop schedule
* 9:00 - 9:15 AM: Introductions
* 9:15 - 10:30 AM: Introduction to compositionality (Mehrbod Estaki & Justin Shaffer)
* 10:30 - 10:45 AM: Break
* 10:45 AM - 12:00 PM: Compositional diversity analysis (Lisa Marotz & Justin Shaffer)
* 12:00 - 1:00 PM: Break
* 1:00 - 2:30 PM: Compositional differential abundance analysis (James Morton)
* 2:30 - 4:00 PM: Compositional, time series / spatial analysis (Cameron Martino)
* 4:00 - 4:50 PM: Parameterizing Songbird & Introduction to BIRDMan (Gibraan Rahman)
* 4:50 - 5:00 PM: Final remarks and Q&A

Workshop materials:
* Workshop notes (this document): tinyurl.com/jketyhwv
* QIIME2 website: qiime2.org
* GitHub page for Songbird: github.com/biocore/songbird
* GitHub page for BIRDMan: github.com/gibsramen/BIRDMAn
* GitHub page for Deicode (RPCA): github.com/biocore/DEICODE
* GitHub page for Gemelli (RPCA & CTF): github.com/biocore/gemelli

Workshop notes:
* Go here and click ‘launch binder’ below ‘q2stats-workshop’: http://github.com/mortonjt/q2stats-workshops This will take a few minutes to load
* Once it loads, go to 'New' and then 'Terminal'
* Follow along with the 'Differential Abundnace' tutorial at the link above
* Need to update by running this in the terminal before running the Songbird command: `pip3 install git+https://github.com/regebro/tzlocal`
* Gibs binders: https://github.com/gibsramen/parameterizing-songbird-demo
https://github.com/gibsramen/BIRDMAn-demo

Discussion points:
* Idea of negative relative abundance values - could they represent sampling effort needed to capture?
* Is microbiome data actually compositional?
* Important to consider the definition of compositionality (e.g., absolute vs. relative abundances)
* Is it necessary to know if feature abundances are going up vs. down?
* Training vs. testing samples
