Agaviromics

This repository contains the code used to perform the downstream statistical analyses in Flores-Nuñez, et al. 2020 in Frontiers in Microbiology.

The datasets generated for this study can be found in the IMG platform, IMG Genome IDs 3300032159, 3300030499, 3300030692, 3300030502, 3300030753, 3300030500, 3300030504, 3300030512, 3300030505, 3300030514, 3300030501, 3300030497, 3300030498, 3300030516, 3300030495, 3300030515, 3300030511, 3300030510, 3300030496, 3300030513.

get_taxacounts.R : Generates the taxonomic profile of the genes of each library, from domain to genus

get_metacounts.R : Generates the functional profile of the genes of each library based on KO annotation

meta_diversity.R : Calculates diversity indexes from raified taxonomic and functional counts

plot_taxacounts.R : Creates barplots and NMDS the taxonomic gene counts

plot_metacounts.R : Creates barplots and NMDS the functional (KO) gene counts

meta_enrichment.R : Performs the enrichment analysis between different subset of grouped samples using edgeR

meta_ova.R : Performs an overrepresentation anaylis of the pathways (KEGG) in each gene enrichment list

meta_AAP.R : Creates abundance plots of aerobic anoxygenic phototrophy related genes

meta_nif.R : Creates abundance plots of nif genes

meta_biofilm.R : Creates abundance plots of biofilm and QS genes