RNA-seq libraries from the MAPPYACTS study sequencing data were aligned with the GRCh38 version of the human transcriptome from the GENCODE project using Salmon v0.9 (Patro et al, 2017) and converted from transcripts to gene expression using the Tximport R package. RNA-seq analysis data of 1375 cancer cell lines were extracted from the DepMap Broad Institute portal. The data were then computed using DEBrowser (Kucukural et al, 2019) and the DESeq2 R package (TMM normalization, parametric fit, LRT test). Coexpression analysis was performed using the network_plot R function.
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