Endangered deep-snow mountain caribou have a distinct winter diet and gut microbiome that may be altered by maternal penning

This repository contains supporting material for the manuscript entitled "Endangered deep-snow mountain caribou have a distinct gut microbiome that may be altered by maternal penning," which is currently being prepared for publication. The R code and terminal required to reproduce all analyses and figures is currently available:

01-otu-seq-processing brings the raw sequencing files into phyloseq objects and performs initial quality filtering and OTU clustering.

02-analyze-controls evaluates the mock community and negative control samples. 

03-statistical-analysis includes code for all statistical analysis described in the manuscript and supplementary material.

04-figures reproduces all the figures and tables in the manuscript.

terminal_scripts includes examples of any code that could not be run in R (e.g., cutadapt, CAZyme annotation).

The sample metadata, including an R workspace with the primary analysis objects, will be made publicly available when the manuscript is accepted or upon reasonable request to the first author ([e-mail]). The original sequencing files have been deposited in the NCBI Short Read Archive (SRA) under BioProject PRJNA1067083.