Prostate_WCM63_paper_figures_2025

This repository contains the code necessary for reproducing the figures and custom analysis in the following manuscript:
Nauseef, J.T., Chu, T.R., Hooper, W.F. et al. A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer. npj Precis. Onc. 9, 91 (2025).
https://doi.org/10.1038/s41698-025-00854-4

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)

  • bamUtils
  • Biostrings
  • boot
  • BSgenome.Hsapiens.UCSC.hg38
  • circlize
  • ComplexHeatmap
  • data.table
  • deconstructSigs
  • dendextend
  • DESeq2
  • dplyr
  • dryclean
  • GenomicRanges
  • ggbeeswarm
  • ggfortify
  • gGnome
  • ggplot2
  • ggpubr
  • ggtree
  • grid
  • gTrack
  • gUtils
  • JaBbA
  • lsa
  • magrittr
  • Matrix
  • optparse
  • parallel
  • patchwork
  • pheatmap
  • RColorBrewer
  • reshape2
  • RSeqLib
  • rtracklayer
  • scales
  • seriation
  • skitools
  • stringr
  • sva
  • treeio
  • UpSetR
  • VariantAnnotation
  • viridisLite

• Other utilities:

  • fragCounter
  • pyclone
  • phyclone
  • ichorCNA