Files in guardant/Zill_2018
The landscape of actionable genomic alterations in cell-free circulating tumor DNA from 21,807 advanced cancer patients
DESCRIPTION
LICENSE
R/ctdna_landscape_analysis.R
R/scatterBarOZ.R
README.md
data_tables_for_figures/alt_per_sample_hist_S1C.csv
data_tables_for_figures/alts_in_high_ctdna_samples_S1D.csv
data_tables_for_figures/brca_oncoprint_table_filtered.csv
data_tables_for_figures/brca_oncoprint_table_unfilt.csv
data_tables_for_figures/cfdna_clonality.RDS
data_tables_for_figures/cnv_ranks.csv
data_tables_for_figures/combined_resistance_table.csv
data_tables_for_figures/crc_oncoprint_table_filtered.csv
data_tables_for_figures/crc_oncoprint_table_filtered_LONG.csv
data_tables_for_figures/crc_oncoprint_table_unfilt.csv
data_tables_for_figures/crc_oncoprint_table_unfilt_LONG.csv
data_tables_for_figures/ct_sum.RDS
data_tables_for_figures/detxn.csv
data_tables_for_figures/df_S10.RDS
data_tables_for_figures/df_akt1_brca.RDS
data_tables_for_figures/df_apc_crc.RDS
data_tables_for_figures/df_arid1a_luad.RDS
data_tables_for_figures/df_braf_crc.RDS
data_tables_for_figures/df_braf_crc_Other_ONLY.RDS
data_tables_for_figures/df_braf_crc_V600E_ONLY.RDS
data_tables_for_figures/df_braf_luad.RDS
data_tables_for_figures/df_braf_luad_Other_ONLY.RDS
data_tables_for_figures/df_braf_luad_V600E_ONLY.RDS
data_tables_for_figures/df_braf_luad_V600E_other.RDS
data_tables_for_figures/df_brca1_brca.RDS
data_tables_for_figures/df_brca2_brca.RDS
data_tables_for_figures/df_cnv_genes.RDS
data_tables_for_figures/df_egfr_brca.RDS
data_tables_for_figures/df_egfr_crc.RDS
data_tables_for_figures/df_egfr_crc_clon2.RDS
data_tables_for_figures/df_egfr_crc_clon2_other.RDS
data_tables_for_figures/df_egfr_drivers_luad.RDS
data_tables_for_figures/df_egfr_luad.RDS
data_tables_for_figures/df_egfr_luad_clon2.RDS
data_tables_for_figures/df_egfr_luad_clon2_L858R.RDS
data_tables_for_figures/df_egfr_res_luad.RDS
data_tables_for_figures/df_erbb2_brca.RDS
data_tables_for_figures/df_erbb2_luad.RDS
data_tables_for_figures/df_esr1_brca.RDS
data_tables_for_figures/df_fig1C.RDS
data_tables_for_figures/df_fig1D.RDS
data_tables_for_figures/df_fig3A.RDS
data_tables_for_figures/df_fig3B.RDS
data_tables_for_figures/df_fig3C.RDS
data_tables_for_figures/df_fig3D.RDS
data_tables_for_figures/df_figS1B.RDS
data_tables_for_figures/df_figS1E.RDS
data_tables_for_figures/df_figS1F.RDS
data_tables_for_figures/df_figS3_breast.RDS
data_tables_for_figures/df_figS3_colo.RDS
data_tables_for_figures/df_figS3_lung.RDS
data_tables_for_figures/df_figS3_prost.RDS
data_tables_for_figures/df_figS6to9.RDS
data_tables_for_figures/df_fusion_luad.RDS
data_tables_for_figures/df_fusion_lung.RDS
data_tables_for_figures/df_jak2
data_tables_for_figures/df_kras_crc.RDS
data_tables_for_figures/df_kras_luad.RDS
data_tables_for_figures/df_met_luad.RDS
data_tables_for_figures/df_nf1_luad.RDS
data_tables_for_figures/df_pik3ca_brca.RDS
data_tables_for_figures/df_pik3ca_crc.RDS
data_tables_for_figures/df_tp53_brca.RDS
data_tables_for_figures/df_tp53_crc.RDS
data_tables_for_figures/df_tp53_luad.RDS
data_tables_for_figures/driver_alt_prevalence_TableS6.tsv
data_tables_for_figures/egfr_counts.Rdata
data_tables_for_figures/egfr_counts_no_t790m.Rdata
data_tables_for_figures/fusion.csv
data_tables_for_figures/genes_muts.RDS
data_tables_for_figures/kras_plot.csv
data_tables_for_figures/luad_oncoprint_table_filtered.csv
data_tables_for_figures/luad_oncoprint_table_unfilt.csv
data_tables_for_figures/monitoring_data.csv
data_tables_for_figures/resistance_freq.RDS
data_tables_for_figures/samples_per_patient.csv
data_tables_for_figures/tp53_counts.Rdata
output/ALK_EML4_grid_plot.pdf
output/ALK_fusion_side.pdf
output/Breast_CNA_ranks_TCGA_vs_GH.pdf
output/CRC_APC_muts_clonal_fraction.pdf
output/CRC_KRASmut_clonality.pdf
output/EGFR_GH_vs_TCGA_freq.pdf
output/EGFR_clonality_LUAD_CRC.pdf
output/EGFR_patient_monitoring_Figure5C.pdf
output/EML4_fusion_side.pdf
output/GH_detxn_rates_092216.pdf
output/Max_VAF_vs_clonal_proportion.pdf
output/NSCLC_KRASmut_clonality.pdf
output/PIK3CA_patient_monitoring_Figure5D.pdf
output/TP53_GH_vs_TCGA_freq.pdf
output/TP53_patient_monitoring_Figure5E.pdf
output/alterations_per_sample.pdf
output/alterations_per_sample_high_ctDNA_overlay.pdf
output/brca.mutex.csv
output/brca_filt.mutex.csv
output/brca_res_barplot.pdf
output/breast_KRASmut_clonality.pdf
output/cfDNA_tests_per_patient.pdf
output/cfDNA_tests_per_patient_FigureS1A.pdf
output/combined_grid_plot.pdf
output/crc.mutex.csv
output/crc_filt.mutex.csv
output/crc_long.mutex.csv
output/crc_long_filt.mutex.csv
output/crc_res_barplot.pdf
output/driver_prevalence_cfDNA_vs_TCGA.pdf
output/luad.mutex.csv
output/luad_filt.mutex.csv
output/nsclc_resistance_barplot.pdf
output/ovarian_KRASmut_clonality.pdf
output/pancreas_KRASmut_clonality.pdf
output/prad_res_barplot.pdf
output/prostate_KRASmut_clonality.pdf
output/sub_CN_per_gene_breast.pdf
output/sub_CN_per_gene_crc.pdf
output/sub_CN_per_gene_lung.pdf
output/sub_CN_per_gene_prostate.pdf
output/sub_CN_vs_VAF_breast.pdf
output/sub_CN_vs_VAF_crc.pdf
output/sub_CN_vs_VAF_lung.pdf
output/sub_CN_vs_VAF_prostate.pdf
output/sub_EGFR_CN_VAF_Figure3A.pdf
output/sub_JAK2_SNVs_table.txt
output/sub_NSCLC_EGFRmut_clonality_NEW.pdf
output/sub_TMB_cfDNA_common_cancers.pdf
output/sub_ctDNA_level_per_indication_adjVAF.pdf
output/sub_ctDNA_level_vs_Num_SSNV_Breast.pdf
output/sub_ctDNA_level_vs_Num_SSNV_CRC.pdf
output/sub_ctDNA_level_vs_Num_SSNV_NSCLC.pdf
