Analysis and visualization of community dynamics in microbial ecology experiments (that use sequence count data) using the truncated Poisson lognormal distribution.
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
Version 0.3 improved the behavior of
It also resolved a conflict between
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
ggplot2, allowing easier manipulation and decoration. OTU tables are
dplyr, allowing easier filtering for interesting OTUs.
This package is mostly a rewording of the
poilog package, designed to make it easier for