Home

Welcome to the microbiomeutilities wiki!

Install microbiomeutilities

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

Template

There is also a Rmarkdown template which can be accessed via the RMarkdown template section.

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.