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,
Rodrguez 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
