Associations between the gut microbiome and metabolome in early life
This repository hosts reproducible scripts for analyses presented in the manuscript workflow for analyses represented in the manuscript "Associations between the gut microbiome and metabolome in early life" by Nguyen et al. 2021+.
Scripts are organized into modularized functions and fed into workflows designed in drake. call the make(plan_name) in the make_<analysis>.R file to execute the workflow. The only exception are the prediction models and Bayesian evaluations, since they are computational intensive and were ran in parallel on Dartmouth's Discovery cluster.
For supplemental picrust2 analyses, pipeline was ran using Snakemake, all files and folders in the picrust2 folder.
plots_ scripts hold all plotting functions.
analysis_ scripts hold all analysis functions.
process_ scripts hold all functions that process outputs from analyses, mostly in service of plotting.
plan_ scripts hold all drake plans for streamlining the dispatch of complex analysis workflow across multiple targets.
Raw data deposited on their respective repositories on NCBI SRA and Metabolomics Data Repository. Dependencies can be accessed using the dependencies.csv file. All Bioconductor packages were installed under Bioconductor version 3.10. R version is 3.6.3.
Currently working on creating a new docker file for increased reproducibility.
To use Docker (WIP) first create an image:
docker build --tag infant_microbiome_metabolome:1.0 .Then boot into interactive mode with RStudio at port 8787
docker run --rm -p 8787:8787 -e PASSWORD=password --name infant_robust infant_microbiome_metabolome:1.0