UrothelialCancer_WGS_paper_figures

This repository contains the code necessary for reproducing the figures and custom analysis in the following manuscript:
Nguyen, D.D., Hooper, W.F., Liu, W. et al. The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution. Nature 635, 219–228 (2024).
https://doi.org/10.1038/s41586-024-07955-3

Dependencies

• R 4.0.0 or greater

• The following R packages (NOTE: not all of these are required for every component. Please see scripts for individual dependencies)

  • optparse
  • ComplexHeatmap
  • circlize
  • viridisLite
  • data.table
  • ggplot2
  • reshape2
  • ggpubr
  • ggrepel
  • gGnome
  • gUtils
  • rtracklayer
  • VariantAnnotation
  • fishhook
  • MutationTimeR
  • plotly
  • deconstructSigs
  • JaBbA
  • parallel
  • Matrix
  • stringr
  • dryclean
  • magrittr
  • GenomicRanges
  • skitools
  • bamUtils
  • BSgenome.Hsapiens.UCSC.hg38

• Other utilities:

  • bedtools
  • samtools
  • LICHeE
  • AmpliconArchitect/AmpliconClassifier
  • minimap2
  • flye