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Welcome to the microbiomeutilities wiki!

Install microbiomeutilities

install.packages("devtools")
devtools::install_github("microsud/microbiomeutilities")

Usually installing microbiome, phyloseq will cover dependencies as these are part of BioC.

Other packages you need to install are:

There are many packages that are useful for overall analysis and I will list a few here. Not all are required for running microbiomeutilites but they may be required for more thorough analysis.

source("http://www.bioconductor.org/biocLite.R")
biocLite(c("ade4", "fastcluster", "df2json", "rjson", "gplots", "ggplot2","MASS","minet","mixOmics", "plyr","qvalue","reshape2","RPA","svDialogs","vegan","WGCNA"))


# from CRAN
install.packages("ggthemes")
install.packages("ggdendro")
install.packages("picante")
install.packages("ggpubr")

Hope this solves the setup. If not then google them and see how to install these packages.