Horseshoe crab microbiome paper supplemental scripts

Description of files

Filename	Description
DESeq2.R	Run differential abundance analysis.
anovas.R	Run between-group significance statistics
barplots.R	Plot barplots (Figures S2-7)
diversityBoxplots.R	Plot alpha diversity box/dotplots (Figure 1)
filtered_table.qza	Qiime2-compatible ASV/OTU table
importTSVPhyseq.R	Utility script for importing data into phyloseq
makeTreeFromDESeqs.sh	Use IQtree to make a tree from DE sequences
plotDESeq2.R	Plot DESeq2 results (Figures 5 and S8)
rep-seqs.qza	Qiime2-compatble representative sequences.
run_this.R	Initialize phyloseq objects contained in folder named "exported"
silva_taxonomy.qza	Qiime2-compatible taxonomy file
tax_glom_fast.R	Faster tax_glom function
top10pie.R	Plot top 10 most abundant genera
top20pie.R	Plot top 20 most abundant genera