Repo for data and analysis for the manuscript Van Syoc et al (in revision). This repository has been archived on Zenodo and is associated with DOI 10.5281/zenodo.10793922
Some data used in these analyses cannot be publicly shared since they were obtained from study authors or institutional Data Use Agreements. Bash scripts to obtain raw metagenomics files and obtain fungal taxonomy are fully reproducible. R scripts for downstream analyses are not reproducible due to data sharing limitations; all files start with a phyloseq object containing fungal taxonomy and metadata but the phyloseq objects are not provided. Therefore, the relative paths used in most of the figure scripts are not useful.
The following analyses are provided:
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Bash scripts to obtain raw metagenomics files from Sequence Read Archive, remove host reads and obtain bacterial and fungal taxonomy..
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Build figure 1.
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Bayesian multinomial logistic-normal linear models (MLN) for T2D-NOMET to NORM and obesity and glycemic metrics.
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Building figure 2.
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MLN for comparison of metformin treatment in T2D.
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Building figure 3.
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MLN comparison of T2D-MET to NORM.
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Mouse study fungal taxonomy, filtering/decontamination, and MLN comparison.
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Building figure 4.