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Consider adding UMAP analysis #444

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cleme opened this issue Nov 17, 2022 · 1 comment
Open

Consider adding UMAP analysis #444

cleme opened this issue Nov 17, 2022 · 1 comment
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AnalysisTools enhancement Summaries Relating to summary generation
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@cleme
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cleme commented Nov 17, 2022

Is your feature request related to a problem? Please describe.
Microbiome data is compositional, which can often lead to biases when using traditional ordination techniques.

Describe the solution you'd like
Consider if we should add UMAP, following https://journals.asm.org/doi/10.1128/mSystems.00691-21

@cleme cleme added enhancement AnalysisTools Summaries Relating to summary generation labels Nov 17, 2022
@cleme cleme added this to the 0.10.0 milestone Nov 17, 2022
@adamcantor22
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We now have access to UMAP as well as TSNE (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7767995/). These are in the latest install of qiime2, accessible with ml qiime/2022.11. Trivial to add to pipeline if desired.

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