Automated transcriptomics data analysis workflow using pathway and network analysis approaches

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.

URL: https://github.com/BiGCAT-UM/COVID19-ZonMw/tree/main/AnalysisNHBECOVID19

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Created: 9th Apr 2021 at 10:54

Last updated: 12th Apr 2021 at 09:34

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