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microbiome / OMA

Orchestrating Microbiome Analysis
https://microbiome.github.io/OMA
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QMP example data #470

Open antagomir opened 4 months ago

antagomir commented 4 months ago

Our new Nat. Medicine publication with Raes Lab Tito et al. (2024) includes QMP profiling data and covariates of general interest (e.g. calprotectin, moisture). The species-level profiles are available as a supplementary table. This will make a good example data on QMP.

Steps to follow:

1) Create an example data set as TreeSE (mia or miaViz - if space will allow); with tree if possible 2) Replicate some of the results for validation 3) Create a section on QMP analyses in OMA

antagomir commented 4 months ago

@ShadmanIshraq could you check if it is possible to load the microbial abundance data and sample metadata from this paper, and create script that arranges it into TreeSummarizedExperiment format? If this works, we could see how to add it as a new demo data set. QMP is essential new approach.

antagomir commented 1 month ago

minimal data is now available in mia https://github.com/microbiome/mia/blob/devel/data/Tito2024QMP.rda