This the respository that contains the code used for bulk RNAseq, scRNAseq, and microbiome analysis.
bulkDESeq.R: This R notebook can be used to reproduce differential gene expression and heatmap construction.
PreprocessTrachAspirate_GITHUBnotations.ipynb: Data was processed and combined into adata ojbect
scVI_GITHUBnotations.ipynb: scVI computation
Clustering_lowclusterforDE_GITHUBannotations.ipynb: clustering (low resolution for entire mono/mac group - saved to take to R)
Clustering_highres_GITHUBannotations.ipynb: higher resolution clustering, cell numbers, UMAPs
Rmarkdown_4GitHub.Rmd: R markdown for pathway, volcano, and heatmaps
The following files contain code used for microbiome analyses.
1_Format_Input_files.html is used to format the input files
2_Coronavirus_percent.html is used to calculate the percent of reads assigned to SARS-CoV-2 in each sample
3_Calculate_Alpha_Beta.html is used to calculate the alpha and beta diversity
4_Heatmap_Top_Vap_Species_byVAPCAT.html is used to generate the heatmaps in Figure 6