R scripts to generate panels from the main figures of Ginno et al., 2024

R version 4.3.0

Required packages: GEOquery, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Mmusculus.UCSC.mm10, GenomicRanges, RColorBrewer, changepoint, Repitools, randtests, Rsamtools, apcluster, regioneR, pheatmap, mixtools, ggplot2, viridis, scales, psych QuasR, Gviz, grid

Processed files: All processed rds files and Phenomex tables can be downloaded within R (code is at the beginning of figures 1 and 2). GEO submission GSE230579. PF1 mutations: GSE230579_PF1_SisterMutations.rds.gz, CAST/C3H liver tumour mutations: GSE230579_F1CastB6_mutations.rds.gz, ATAC peaks table in PF1: GSE230579_PF1_ATAC_Peaks.rds.gz, RNA genic counts in PF1: GSE230579_PF1_RNA_counts.rds.gz

BAM file generation: Raw sequencing data for PF1 sisters and Mus castaneus x C3H tumours are in SRA submission PRJNA934746. Alignment parameters for generating and filtering bam files from raw sequencing data are described in materials and methods under the subheadings "Whole genome and ATAC alignment and filtering", "Dual-hybrid N-masked reference for WGS F1 tumour haplotype discrimination" and "PF1 RNA-seq data processing and analysis". Bam files will need to be generated to produce Figure 3, 4a and 4g.

Phenomex files: Tables of cell counting and FUCCI fluorophore imaging on the Phenomex platform are included in this repository and code for downloading the files is included in figure 1.