All analysis was performed using custom scripts in R version 3.6.3 using the DESeq2 version 1.26.0 framework59. Correspondence between lanes was first confirmed by principal component analysis before merging counts using the command collapseReplicates(). One outlier sample from the Other Pneumonia group with low RIN score and exhibiting extreme deviation on PCA and poor alignment and assignment metrics was excluded from downstream analysis. For differential expression analysis (DEA), both proportion of alveolar macrophage from flow cytometry data and diagnosis were used as explanatory factors. A “local” model of gene dispersion was employed as this better fit dispersion trends without obvious overfitting, and gene outlier replacement was disabled; otherwise default settings were used. See code for details.

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