ProstateBrainMet_WGS_paper_figures

This repository contains the code necessary for reproducing the figures and custom analysis in the following manuscript:
Evolution of Structural Rearrangements in Prostate Cancer Intracranial Metastases: Khani, F., Hooper, W.F., Wang, X. et al. Evolution of structural rearrangements in prostate cancer intracranial metastases. npj Precis. Onc. 7, 91 (2023).
https://doi.org/10.1038/s41698-023-00435-3

Dependencies

• R 3.6.1 or greater

• The following R packages (for figures 2-4)

  • circlize
  • ComplexHeatmap
  • GenomicRanges
  • ggalluvial
  • gGnome
  • ggplot2
  • gTrack
  • gUtils
  • MutationTimeR
  • optparse
  • patchwork
  • reshape2
  • stringr
  • VariantAnnotation

• The following R packages (for figure 5 analysis + plotting)

  • biomaRt
  • circlize
  • ComplexHeatmap
  • DESeq2
  • dplyr
  • EnvStats
  • ggplot2
  • ggpubr
  • ggrepel
  • limma
  • lsa
  • matrixStats
  • NanoStringQCPro
  • pheatmap
  • readxl
  • rstatix
  • RUVSeq
  • stringr
  • survival
  • survminer
  • tidyr
  • writexl
  • xlsx