Study title: Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets

Authors: Jueeli D. Vaidya, Sanne van Gastelen, Hauke Smidt, Caroline M. Plugge, Joan E. Edwards

Correspondence: Hauke Smidt (hauke.smidt[at]wur.nl)

This repository contains codes for analysis done in the research article by Vaidya JD, et al (2019) Characterization of dairy cow rumen bacterial and archaeal communities associated with grass silage and maize silage based diets. Under review. XX.

Structure:
Vaidya_JD_2019_RumenDietMicrobiome
project folder:

Structure:  
Vaidya_JD_2019_RumenDietMicrobiome/ # Main repository  
                     |---- archaea_analysis.RMD # Codes for analysis of Archaeal data.   
                     |---- bacterial_analysis.RMD # Codes for analysis of Bacterial data.   
                     |---- input/ # Filtered cleaned Phyloseq objects for bacterial and archaeal community analysis.  
                              |--- pseq_archaea.rds  
                              |--- pseq_bacteria.rds  

Instructions

1. Download the repo and unzip.
2. Open Rumen diet data analysis.Rproj in RStudio.
3. Open archaea_analysis.RMD and click knit.
4. Open bacterial_analysis.RMD and click knit.