This repository contains the analysis code for Noecker et al, "Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies" (submitted).
Contents:
FBA_functions.R: A library of functions for processing and analyzing simulation data and performing analyses related to this work.mainDatasetContributionsCorrelations.Rmd: A notebook of analyses of the main simulation dataset described in the manuscript, including the code to generate Figures 1-4 and S1-S6.variedSimulations_correlationResults.Rmd: A notebook of analyses of the simulation datasets with varied nutrient inflow, including the code to generate Figures 5 and S9.LengthVaried_Simulations_correlationResults.Rmd: Analysis of simulations of varying duration. Includes the code to generate Figure S7.vmaxVaried_Simulations_correlationResults.Rmd: Analysis of simulations with a varying maximum rate of reaction (vmax). Includes the code to generate Figure S8.ContributionDefinition_fluxInstantaneous.Rmd: Analysis of the original ten-species dataset and simulations of longer duration using an alternative definition of contribution values.HMPContributionsCorrelations.Rmd: Analysis of simulations of 57 HMP-based communities. Includes the code to generate Figure 6 and Figure S10.mimosaMainRun.Rmd: A notebook documenting MIMOSA analysis of the simulation dataset, using both full model and the KEGG approximation. Includes the code to generate Figure 7.
The input data files to re-run the analyses are available as Supplementary Data 1 and at http://borensteinlab.com/download.html. Save each sheet of the spreadsheet as a text file in the same directory. In order to run new simulations, you will need to separately download the pipeline code from http://borensteinlab.com/download.html.