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How to compare RNA expression correlation?

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!

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rna-seq cancer-cell-line correlation
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written by Wang Cong • Wang Cong

1 answer

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

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written by Trivas • Trivas

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