This repository implements the hypothesis testing method to identify contaminants, including tcontam for high microbial biomass and tcontamL for low or mixed microbial biomass.
To install the decontam R package with the tcontam and tcontamL implementation, you need to install through the Github using the devtools package:
library(devtools)
devtools::install_github("hczdavid/decontam")We demonstrate the usage of tcontam and tcontamL, and compare the performance with current decontam method using simulation and two real microbiome datasets.
Oral microbiome dataset analysis
The data used for these analyses can be found at the tcontamManuscript repository.
Bugs and difficulties in using decontam are welcome on the issue tracker.
Planned feature improvements are also publicly catalogued at on the "Issues" page for decontam: https://github.com/benjjneb/decontam/issues