HOB_Enrichment

Repository for data analyses scripts of Hu et al. (2019)

Files

Script Filename	Content
Heatmaps_and_Ordinations.R	main script for drawing multiple heatmaps and ordination plots
DataLoader.R	separate script to preload and wrangle the data for DE_testing.R (is included in Heatmaps_and_Ordinations.R)
DE_testing.R	DESeq2 differential abundance testing, knitr spin compatible

Dependencies

All data was analyzed in R (v 3.6.1.). The following additional packages should be installed to run the provided code:

• ggplot2 (CRAN)
• extrafont (CRAN)
• phyloseq (BioConductor)
• NMF (CRAN)
• vegan (CRAN)
• gplots (CRAN)
• readxl (CRAN)
• DESeq2 (BioConductor)
• data.table (CRAN)
• splitstackshape (CRAN)
• dplyr (CRAN)
• scales (CRAN)
• ape (CRAN)