Differential Expression and Enrichment Analysis
The raw counts from the SARS-coV-2 transcriptomic profiles were subjected to differential expression analysis by DESEq2 v1.26.0 . Subsequently the genes were pre-ranked using the p-values from DESeq2 analysis and subjected to pre-ranked gene set enrichment analysis (GSEA) . Gene sets with FDR <0.05 were considered to be statistically significant and were visualized using EnrichmentMap plugin of Cytoscape . For drug signatures from iLINCS, differentially expressed genes with p<0.05 were considered to be statistically significant. Enrichment of kinase perturbation was carried out using Enrichr .