The scripts in the lungbiome repository provide the complete underlying code for the analysis and figures in the following manuscript:
Shankar J. et al. Looking beyond respiratory cultures: Microbiome-cytokine signatures of bacterial pneumonia and tracheobronchitis in lung transplant recipients. Am J Transplant. Wiley Online Library; 2015; Available from: http://dx.doi.org/10.1111/ajt.13676
For model specifications, underlying theory as well as a comparative evaluation of BMA ensemble regression against other ensemble regression models, please review:
Shankar J. et al. A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses. BMC Bioinformatics. 2015 Feb;16(1):31+. DOI:10.1186/s12859-015-0467-6. Available at: http://dx.doi.org/10.1186/s12859-015-0467-6.
Citing lungbiome
Shankar J. et al. Looking beyond respiratory cultures: Microbiome-cytokine signatures of bacterial pneumonia and tracheobronchitis in lung transplant recipients. Am J Transplant. Wiley Online Library; 2015; Available from: http://dx.doi.org/10.1111/ajt.13676
BibTeX
@ARTICLE{Shankar2015Looking,
title = "Looking beyond respiratory cultures: Microbiome-cytokine
signatures of bacterial pneumonia and tracheobronchitis in lung
transplant recipients",
author = "Shankar, Jyoti et al.",
journal = "American journal of transplantation: official journal of the
American Society of Transplantation and the American Society of
Transplant Surgeons",
publisher = "Wiley Online Library",
year = 2015,
url = "http://dx.doi.org/10.1111/ajt.13676",
issn = "1600-6135"
}