Consider adding UMAP analysis

clemente-lab / mmeds-meta

A database for storing and analyzing omics data

https://mmeds.org

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Consider adding UMAP analysis #444

Open cleme opened 2 years ago

cleme commented 2 years ago

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

adamcantor22 commented 1 year ago

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.