├── .DS_Store ├── README.md ├── crypt_fission ├── Crypt fission rate - main.docx ├── README.txt ├── abc_function_archive.r ├── abc_simulation_worker.r ├── biopsy_data_combined.txt ├── cfr_accepted_sims_excl4yr_July_Upd[2].txt ├── crypt_fission_rate_gt_0.05_lt_0.1.txt ├── crypt_fission_rate_gt_0.15_lt_0.2.txt ├── crypt_fission_rate_gt_0.1_lt_0.15.txt ├── crypt_fission_rate_lt_0.05.txt ├── crypt_fission_rate_methods.docx ├── draw_priors.r ├── estimate_posterior.r ├── extract_event_counts.r ├── find_observed_coalescence_times.r ├── preprocess_spatial_matrices.r ├── prior_and_post_distr_July_Upd.png ├── prior_used.txt ├── run_abc_simulation.sh ├── run_abc_simulation_worker.sh ├── run_extract_event_counts.sh └── sim_sumStats_excl4yr_July_Upd.txt ├── files_added_post_publication ├── ID_novel_sig_trinucs.txt ├── Key_matching_Ids.csv ├── SBS_novel_sig_trinucs.txt ├── Subs_by_crypts_modelling_crypts.txt.zip └── test ├── signature_extraction ├── dbses_hdp_signature_extraction │ ├── PCAWG_sigProfiler_DBS_signatures.txt │ ├── dbs_category_counts.txt │ └── hdp_dbs.R ├── indels_hdp_signature_extraction │ ├── .DS_Store │ ├── ID_category_counts.txt │ ├── PCAWG_sigProfiler_ID_signatures.csv │ └── hdp_id.R ├── instructions └── subsitutions_hdp_signature_extraction │ ├── PCAWG_sigProfiler_SBS_signatures.csv │ ├── SBS_EM_to_share_out_sigs.R │ ├── hdp_extract_signature_results.R │ ├── hdp_sbs.R │ └── sbs_category_counts.txt └── stem_cell_number_and_replacement_rate ├── colon_stem_cell_abc_simulator.R └── input_files ├── PD37590b_lo0009_input_data.txt ├── PD37590b_lo0016_input_data.txt ├── PD37590b_lo0018_input_data.txt ├── PD37590b_lo0020_input_data.txt ├── PD37590b_lo0028_input_data.txt ├── PD37590b_lo0042_input_data.txt ├── PD37590b_lo0048_input_data.txt ├── PD37590b_lo0058_input_data.txt ├── PD37590b_lo0084_input_data.txt ├── PD37590b_lo0092_input_data.txt ├── PD37590b_lo0105_input_data.txt ├── PD37590b_lo0107_input_data.txt ├── PD37590b_lo0108_input_data.txt ├── 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