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How can I make a similar mutated gene expression figure with TCGA data

Student just starting out in a cancer genomics lab. I have a paper in which I am interested in replicating the first figure to get a grasp on the techniques used, but unsure what steps I need to take. I would like to use TCGA data from FireBrowse to do this. I already have the mutation annotation file (MAF) and RNA-seq (genes normalized) file downloaded for breast cancer. Do I need to download any additional or alternative files? How should I go about replicating this figure, any good resources for the analyses I need to do? I have R installed, but other than that I have no idea where to start. Figure 1 from this paper

cancer rna-seq firebrowse tcga
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updated by tomas4482 • tomas4482 • written by valgenome • valgenome

1 answer

maftools or ComplexHeatmap R package is a good start.

ComplexHeatmap

maftools

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written by tomas4482 • tomas4482

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