TEXMEX

Treatment Effect eXplorer for Microbial Ecology eXperiments
by Scott W Olesen and Eric J Alm
texmex
DESCRIPTION
texmex is an software package (implemented in R and Python 3) designed to help visualize and interpret community dynamics observed in microbial ecology experiments that use sequencing count data. Given one inoculum split into two replicates, one control and one experimental, which OTUs are growing or shrinking in response to the treatment? texmex is designed to help account for changes in the control unit's community composition as well as dampen compositional effects that might occur in either unit.

INSTALLATION
You can install this package in R using install.packages('texmexseq'). The package includes demos and an example data set. The Python version of the code includes installation instruction.

REFERENCE
Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez J, et al. (2016) A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments. PLoS ONE 11(5): e0154804. doi:10.1371/journal.pone.0154804

R SOURCE
The source for the model run in the paper:
CRAN page
github page

PYTHON SOURCE
github page