How to compare RNA expression correlation?

Question

[Wang Cong]

I have a set of genes that is important for the cell cycle and DNA damage. I wish to compare the RNA expression of these genes between each two cell lines and generate a heatmap to visualize the correlation (the x and y axis are all types of cancer cell lines). May I ask if there are any software/packages to do this task? Thanks!

Answer 1

[Trivas]

You'll want to use a differential gene expression software (DESeq2, edgeR, etc.) then take the output or normalized counts for downstream analyses. I like using the package ComplexHeatmap since it's easier to customize than pheatmap