This repository contains scripts used for RNA-seq data analysis (Figures 2 and S4) and parameter inference in mathematical models (Figures 1, 5, and S7) in the manuscript:

Feng et al "Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions", submitted for publication in Cell Host & Microbe.

Description:

• Subfolder "Scripts_RNAseq": Python and R scripts used to process RNA sequencing data from raw fastq files.

• Subfolder "Scripts_Figure_1B": MATLAB scripts that use adaptive Markov Chain Monte Carlo (MCMC) method to infer growth parameters (i.e., growth rate and carrying capacity) from single strain growth data in different glycans.

• Subfolder "Scripts_Figure_5C": MATLAB scripts to obtain the linear regression model for butyrate production.

• Subfolder "Scripts_Figures_5A-B_S7A": MATLAB scripts that use adaptive MCMC to infer interspecies interaction parameters and growth parameters in generalized Lotka-Volterra (gLV) models using co-culture experimental data in different glycans.