├── .gitmodules ├── README.md └── code_figures_paper ├── README.md ├── figure_1b ├── README.txt ├── figure_1b.R └── wgd.status.txt.gz ├── figure_1c ├── README.txt ├── figure_1c.R └── summary_stats_agreement.txt.gz ├── figure_1d ├── README.txt ├── figure1d.R ├── pcawg_similarities_before_MTimer_no_wcc.Rdata.gz └── simclone1000_similarities_with_truth_before_MTimer_noWCC.Rdata.gz ├── figure_2bc ├── README.txt ├── consensus.20170217.purity.ploidy.txt.gz ├── figure_2bc.R ├── pcawg_weme2018_final.txt.gz └── pcawg_weme2018_wcc_final.txt.gz ├── figure_3 ├── .DS_Store ├── README.txt ├── figure3.input.txt.gz ├── figure_3.R └── pcawg.colour.palette.R ├── figure_4a-df ├── .fuse_hidden0000047e00000002 ├── README.txt ├── additionalITH_phasingresults.tsv.gz ├── figure_4a-df.R └── pcawg.colour.palette.R ├── figure_4eg ├── README.txt ├── Tx100MutbBurden.tsv.gz ├── Tx100TreesCRUK.rda.gz └── figure_4eg.R ├── figure_4h ├── MSAI_EOPC-DE_BAF-LogR_randomised.RDS ├── MSAI_EOPC-DE_samples_regions.tsv └── figure_4h.R ├── figure_5 ├── README.txt ├── Stats.csv.gz ├── TableS3_panorama_driver_mutations_pcawg_annotated_v1.1.tsv.gz ├── additional_stats.RData.gz ├── barplot_supported_boudaries.r ├── consensus_subclonal_reconstruction_v1.1_20181121_structures.txt.gz ├── consensus_subclonal_reconstruction_v1.1_20181121_summary_table.txt.gz ├── encoding.R ├── figure_5.R ├── individual_tumours_CLL_with_bootstraps.RData.gz ├── make_summary_plots.R ├── pcawg.wg11.final_sample_list.txt.gz ├── sig_colors.sigProfiler.RData.gz ├── signature_annotations.txt.gz ├── signature_trajectories.tar.gz ├── summarise.R ├── supported_boundaries_info.RData.gz ├── traj_CLL.RData.gz ├── traj_means_all_cancer_types_list.RData.gz └── util.R ├── figure_6a ├── .DS_Store ├── README.txt ├── cancer_type.gene.list.txt.gz ├── cancer_type.sv.list.txt.gz ├── figure_6.snv.input.txt.gz ├── figure_6.sv.input.txt.gz ├── figure_6a.R ├── proportions_of_drivers_per_SRB.txt.gz └── snv.driver.txt.gz ├── figure_6bc ├── Figure6b.R ├── Figure6c.R ├── README.txt ├── aGB.032019.Rda.gz ├── colourPalette.R ├── pcawg.wg11.final_sample_list.txt.gz └── summary_table_combined_annotations_v4.txt.gz ├── figure_6e ├── ._pcawg.wg11.final_sample_list.txt ├── README.txt ├── TableS3_panorama_driver_mutations_pcawg_annotated_v1.1.tsv.gz ├── TableS3_panorama_driver_mutations_pcawg_clinically_actionable_events.tsv.gz ├── all_annotated_snvIndel_proteinChanging.txt.gz ├── figure_6e.R ├── pcawg.wg11.final_sample_list.txt.gz └── summary_table_combined_annotations_v3.txt.gz ├── suppfigure_1 ├── .DS_Store ├── README.txt ├── TCGAsamples.consensus_purity.txt.gz └── figure_S1.R ├── suppfigure_2a ├── .DS_Store ├── README.txt ├── figure_S2a.R └── nrpcc.summary_table.txt.gz ├── suppfigure_2b ├── .DS_Store ├── README.txt ├── figure_S2b.R └── nrpcc.summary_table.txt.gz ├── suppfigure_2c ├── .DS_Store ├── README.txt ├── figure_S2c.R ├── input.figureS3c.txt.gz └── pcawg.colour.palette.R ├── suppfigure_3 ├── DPClust_EOPC-DE_results.tsv.gz ├── 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