How can I make a similar mutated gene expression figure with TCGA data
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Entering edit mode
12 months ago
valgenome • 0

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 • 438 views
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Entering edit mode
12 months ago
tomas4482 ▴ 390

maftools or ComplexHeatmap R package is a good start.

ComplexHeatmap

maftools

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