Analyses (R scripts and Quarto documents) pertaining to the manuscript "Microbiota effects and predictors of Lactobacillus crispatus colonization after treatment with a vaginal live biotherapeutic: results from a randomized, double-blinded, placebo-controlled trial" by Bloom, Symul, et al., 2025. MedRxiv doi: https://doi.org/10.1101/2025.08.18.25333897
Directories 00-02 contain scripts for data cleaning, pre-processing, and assembly into a Bioconductor MultiAssayExperiment object.
Directory 03 contains sub-directories organized to roughly match the order analyses are presented in the associated manuscript.
R functions used across all analysis steps are in the R/ directory located at the repo root. R functions specific to some analyses are located in the corresponding sub-directories.
Processed and integrated data is deposited on Zenodo: https://zenodo.org/records/17755173