| 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 |