VIBRANT trial: analyses and scripts used for data quality control and integration of modalities into a single MultiAssayExperiment R object

This entry provides the code (.qmd files), associated rendering (.html), and R scripts (R * /*.R files) used to check, clean, format, transform, and harmonize data from the different biological assays (metagenomics, 16S amplicon sequencing, luminex, etc.) and CRF survey data for the VMRC VIBRANT trial. There is one (or a few) quarto documents (.qmd) per modality (clinical/survey data or assays). While most documents are standalone, they were designed to be read and executed in the order they are numbered. These documents read "raw tabular data" from private, secure shared drives and export the processed data on secure shared drives. From 90_... the individual assays are merged into a single MultiAssayExperiment R object, which is then augmented and exported for downstream analyses. Finally, note that while these documents are regularly "rendered" to html files, the "rendering date" shown on the html files may not always reflect the latest changes in the code. Most of these files have not been modified since mid-June 2025. Please check the GitHub version history for the latest changes.