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qiime2 / cancer-microbiome-intervention-tutorial

JupyterBook for QIIME 2 FAES January 2022 workshop
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NEW: alpha diversity tutorial with LME #43

Closed ebolyen closed 2 years ago

ebolyen commented 2 years ago

Doc build failure is a result of a stale env, that should self-correct soon.

thermokarst commented 2 years ago

New env files are up, I just triggered a rebuild.

ebolyen commented 2 years ago

Thanks for the review @gregcaporaso!

Re: protocol vs transplant, that makes a lot of sense. I had definitely misunderstood where the effect was. That was also the reason I went with HCT instead of FMT in the final plot (which looked fine, but FMT is actually even better, as you expect).

I can make these changes.

Here's the final model FMT generates (filename is wrong, since it was from an earlier revision before I went with HCT): https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fdl.dropbox.com%2Fs%2Fid4xm95pf8mrm0o%2Flme-obs-features-interactions%25281%2529.qzv%3Fdl%3D1

ebolyen commented 2 years ago

Latest updates require this to have propagated into an env: https://github.com/qiime2/q2cli/pull/275 So tune in tomorrow I guess.