Critically ill COVID-19 patients exhibit peripheral immune profiles predictive of mortality and reflective of SARS-COV-2 viral burden in the lung
In our analysis of critically ill COVID-19 patients, we have utilized custom code in several instances. Specifically, we have written code to:
a) enable discovery of cell type specific gene modules in peripheral blood mononuclear cells; b) utilize cell type specific gene modules to predict outcome; and c) definition of a transcriptional signature of infected myeloid cells in the lower respiratory tract.
In most instances, we have not developed new computational methods but rather are leveraging parts of the extensive ecology of R packages available for analysis of scRNAseq data and for machine learning. The examples of custom code included will facilitate usage of similar approaches.