Treatment Effect eXplorer for Microbial Ecology eXperiments that use sequence counts (aka texmexseq) is an R package designed to normalize OTU count data and correct for community composition changes that are common to a control and experimental unit.
There is a demo of the code in the demo folder of the source distribution. The Example sections of the help pages for the functions in the package also have working commands.
The package in on CRAN, so it should be as easy as install.packages('texmexseq').
Version 0.3 improved the behavior of z.transform.table and f.transform.table. It also resolved a conflict between dplyr and testthat.
Version 0.2 is a non-backward-compatible rework of version 0.1. The underlying theory and computational methods are the same. Rather than creating Pair and Quad functions, the transformations are made directly to the OTU tables. Plots are made using ggplot2, allowing easier manipulation and decoration. OTU tables are manipulated using dplyr, allowing easier filtering for interesting OTUs.
This package is mostly a rewording of the poilog package, designed to make it easier for microbial ecologists.
GPL-3