The R scripts are short and quick pipelines on analyzing microarray raw data and RNA-seq count data utilized in the paper entitled "Systems biomedicine of primary and metastatic colorectal cancer reveals potential therapeutic targets". DEGs obtained from analyzing genomic datasets were used to construct the PPI network. Then, a shortest-path-based network analysis flowchart were introduced in the article to extract a smaller network called core network from the PPI network. Nodes in the core network then verified by multiple validation datasets, survival analysis and expression profiling. Expression of validated genes were proposed as the therapeutic targets for colorectal cancer treatment.