Additional file 15 of 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

Additional file 15: R Script for DESeq2 and phyloseq analyses. R script to perform MAG and KO level using the likelihood ratio test (LRT) in DESeq2. Analyses identify significantly differentially abundant MAGs and KOs when the more restrictive 40% and 60% MER diet treatments are contrasted against the 80% MER diet treatment. Statistical analysis of the ruminal community structure is performed using the Adonis2 PERMANOVA analysis. Principal coordinate analysis (PCoA) and canonical analysis of principal coordinates (CAP) ordination plots are generated using phyloseq and ggplot2.