GitHub - reimandlab/CA2M: Chromatin accessibility of primary human cancers ties regional mutational processes with tissues of origin (repository for paper)

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Chromatin accessibility of primary human cancers ties regional mutational processes with tissues of origin (repository for paper)

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
.ipynb_checkpoints		.ipynb_checkpoints
000_HEADER.R		000_HEADER.R
001A_process_Roadmap_data.R		001A_process_Roadmap_data.R
001B_process_ATACSeq.R		001B_process_ATACSeq.R
001C_process_PCAWG_MAF.R		001C_process_PCAWG_MAF.R
001D_process_PCAWG_intowindows.R		001D_process_PCAWG_intowindows.R
001E_process_vierstra_bigwigs.R		001E_process_vierstra_bigwigs.R
001F_process_RepliSeq_tracks.R		001F_process_RepliSeq_tracks.R
001G_get_SBS_SIG_for_PCAWG_MAF.R		001G_get_SBS_SIG_for_PCAWG_MAF.R
001H_process_mut_sig_RMV_PANCAN.R		001H_process_mut_sig_RMV_PANCAN.R
001I.sh		001I.sh
001I_process_mut_sig_RMV.R		001I_process_mut_sig_RMV.R
001J_mutvsCA_landscape_plots.R		001J_mutvsCA_landscape_plots.R
001K_muttrack_cormaps.R		001K_muttrack_cormaps.R
001L_CA_RT_associations.R		001L_CA_RT_associations.R
001M_CAvsCAplusRT.R		001M_CAvsCAplusRT.R
001N_mutvsCA_RT_landscape.R		001N_mutvsCA_RT_landscape.R
001O_get_muttiming_tracks.R		001O_get_muttiming_tracks.R
001P_getmutVAF_tracks.R		001P_getmutVAF_tracks.R
002A.sh		002A.sh
002A_run_allprimary_RF.R		002A_run_allprimary_RF.R
002B.sh		002B.sh
002B_run_normaldnase_RF.R		002B_run_normaldnase_RF.R
002C_plot_normalvstumour_R2_barplots.R		002C_plot_normalvstumour_R2_barplots.R
002D.sh		002D.sh
002D_run_tumorCAplusRT.R		002D_run_tumorCAplusRT.R
002E.sh		002E.sh
002E_run_normalCAplusRT.R		002E_run_normalCAplusRT.R
002F_plot_CART_normalvstumor.R		002F_plot_CART_normalvstumor.R
002G_get_window_errors_tumourCA+RT_RF.R		002G_get_window_errors_tumourCA+RT_RF.R
002H_get_window_errors_normalCA+RT_RF.R		002H_get_window_errors_normalCA+RT_RF.R
002I_plot_facetwrap_errorplots.R		002I_plot_facetwrap_errorplots.R
003A_get_feature_importances.R		003A_get_feature_importances.R
003B.sh		003B.sh
003B_run_featureimportance_permutations.R		003B_run_featureimportance_permutations.R
003C.sh		003C.sh
003C_RF_bootstrap_importances.R		003C_RF_bootstrap_importances.R
003D_toppred_barplots.R		003D_toppred_barplots.R
003E_top_pred_facet_barplots.R		003E_top_pred_facet_barplots.R
003F_run_SHAP_RF.R		003F_run_SHAP_RF.R
003G_plot_toppred_SHAP.R		003G_plot_toppred_SHAP.R
003H_SHAP_CA_densityplots.R		003H_SHAP_CA_densityplots.R
004A.sh		004A.sh
004A_run_mut_sig_RF.R		004A_run_mut_sig_RF.R
004B.sh		004B.sh
004B_run_permtest_sig_importances.R		004B_run_permtest_sig_importances.R
004C.sh		004C.sh
004C_run_bootstraptest_sig_importances.R		004C_run_bootstraptest_sig_importances.R
004D.sh		004D.sh
004D_run_mutsig_RFSHAP.R		004D_run_mutsig_RFSHAP.R
004E_mutsig_etiology_boxplots.R		004E_mutsig_etiology_boxplots.R
004F_mutsig_predim_facetbarplot.R		004F_mutsig_predim_facetbarplot.R
004G_mutsig_SHAP_plots.R		004G_mutsig_SHAP_plots.R
004H_mutisg_predimp_barplots.R		004H_mutisg_predimp_barplots.R
005A.sh		005A.sh
005A_run_RF_100KB_windowerrors.R		005A_run_RF_100KB_windowerrors.R
005B_ploterror_histograms.R		005B_ploterror_histograms.R
005C_get_window_pvals.R		005C_get_window_pvals.R
005D_get_full_manhattan_plot.R		005D_get_full_manhattan_plot.R
005E_get_errors_forgenes.R		005E_get_errors_forgenes.R
005F_windowxcancertype_heatmap.R		005F_windowxcancertype_heatmap.R
005G_runAP_siggenes.R		005G_runAP_siggenes.R
999_process_data.R		999_process_data.R
999_run_RF_withSHAP.R		999_run_RF_withSHAP.R
999_run_randomforest_experiment.R		999_run_randomforest_experiment.R