In this study, we developed an automated and reproducible workflow for transcriptomics data analysis using network biology approaches. The analyses are fully automated in R with clusterProfiler and RCy3 to connect to the widely adopted network analysis software Cytoscape including the CyTargetLinker app for network extension. For demonstration, we use a publicly available dataset from Blanco-Melo et al., GSE147507 obtained from GEO. After pre-processing with DESeq2, the dataset contains log2 fold changes, p-values, and adjusted p-values of 21,797 genes from the human lung epithelial cell line NHBE comparing expression levels before and after SARS-CoV-2 infection.
The script is available on Github repository.
Created: 9th Apr 2021 at 10:54
Last updated: 12th Apr 2021 at 09:34