├── README.md ├── clonality_pre_post ├── README.md ├── clonality.analysis.R ├── clonality.surv.R └── clonality.utils.R ├── data ├── CountData.BMS038.txt ├── README.md ├── SampleTableCorrected.9.19.16.csv ├── TableS6B_GeneExcluded.csv ├── bms038_clinical_data.csv ├── clonality.data.table.pyclone.95.ci.txt ├── genomic_data_per_case.csv ├── pre_therapy_nonsynonmous_mutations.csv ├── pyclone │ └── pre │ │ ├── Pt102_pre.loci.ci95.tsv │ │ ├── Pt103_pre.loci.ci95.tsv │ │ ├── Pt106_pre.loci.ci95.tsv │ │ ├── Pt108_pre.loci.ci95.tsv │ │ ├── Pt10_pre.loci.ci95.tsv │ │ ├── Pt11_pre.loci.ci95.tsv │ │ ├── Pt13_pre.loci.ci95.tsv │ │ ├── Pt17_pre.loci.ci95.tsv │ │ ├── Pt18_pre.loci.ci95.tsv │ │ ├── Pt23_pre.loci.ci95.tsv │ │ ├── Pt25_pre.loci.ci95.tsv │ │ ├── Pt26_pre.loci.ci95.tsv │ │ ├── Pt27_pre.loci.ci95.tsv │ │ ├── Pt28_pre.loci.ci95.tsv │ │ ├── Pt29_pre.loci.ci95.tsv │ │ ├── Pt30_pre.loci.ci95.tsv │ │ ├── Pt31_pre.loci.ci95.tsv │ │ ├── Pt32_pre.loci.ci95.tsv │ │ ├── Pt34_pre.loci.ci95.tsv │ │ ├── Pt37_pre.loci.ci95.tsv │ │ ├── Pt38_pre.loci.ci95.tsv │ │ ├── Pt3_pre.loci.ci95.tsv │ │ ├── Pt44_pre.loci.ci95.tsv │ │ ├── Pt46_pre.loci.ci95.tsv │ │ ├── Pt47_pre.loci.ci95.tsv │ │ ├── Pt48_pre.loci.ci95.tsv │ │ ├── Pt49_pre.loci.ci95.tsv │ │ ├── Pt4_pre.loci.ci95.tsv │ │ ├── Pt51_pre.loci.ci95.tsv │ │ ├── Pt52_pre.loci.ci95.tsv │ │ ├── Pt53_pre.loci.ci95.tsv │ │ ├── Pt58_pre.loci.ci95.tsv │ │ ├── Pt59_pre.loci.ci95.tsv │ │ ├── Pt5_pre.loci.ci95.tsv │ │ ├── Pt60_pre.loci.ci95.tsv │ │ ├── Pt65_pre.loci.ci95.tsv │ │ ├── Pt66_pre.loci.ci95.tsv │ │ ├── Pt67_pre.loci.ci95.tsv │ │ ├── Pt68_pre.loci.ci95.tsv │ │ ├── Pt70_pre.loci.ci95.tsv │ │ ├── Pt72_pre.loci.ci95.tsv │ │ ├── Pt73_pre.loci.ci95.tsv │ │ ├── Pt74_pre.loci.ci95.tsv │ │ ├── Pt76_pre.loci.ci95.tsv │ │ ├── Pt77_pre.loci.ci95.tsv │ │ ├── Pt79_pre.loci.ci95.tsv │ │ ├── Pt7_pre.loci.ci95.tsv │ │ ├── Pt82_pre.loci.ci95.tsv │ │ ├── Pt83_pre.loci.ci95.tsv │ │ ├── Pt84_pre.loci.ci95.tsv │ │ ├── Pt85_pre.loci.ci95.tsv │ │ ├── Pt86_pre.loci.ci95.tsv │ │ ├── Pt87_pre.loci.ci95.tsv │ │ ├── Pt89_pre.loci.ci95.tsv │ │ ├── Pt8_pre.loci.ci95.tsv │ │ ├── Pt90_pre.loci.ci95.tsv │ │ ├── Pt92_pre.loci.ci95.tsv │ │ ├── Pt94_pre.loci.ci95.tsv │ │ ├── Pt98_pre.loci.ci95.tsv │ │ └── Pt9_pre.loci.ci95.tsv ├── rld.BMS038.20171011.csv ├── survival.data.clonal.pyclone.0.95.TRUE.txt └── tcr │ ├── Immunoseq.tgz │ ├── KDEfiles │ ├── Pt103_KDE.csv │ ├── Pt106_KDE.csv │ ├── Pt108_KDE.csv │ ├── Pt23_KDE.csv │ ├── Pt30_KDE.csv │ ├── Pt31_KDE.csv │ ├── Pt34_KDE.csv │ ├── Pt44_KDE.csv │ ├── Pt48_KDE.csv │ ├── Pt52_KDE.csv │ ├── Pt59_KDE.csv │ ├── Pt5_KDE.csv │ ├── Pt67_KDE.csv │ ├── Pt82_KDE.csv │ ├── Pt93_KDE.csv │ └── README.md │ ├── README.md │ ├── TCRmetrics.csv │ └── aaCDR3perVJ │ ├── Pt10_on_aaCDR3perVJ.tsv │ ├── Pt10_pre_aaCDR3perVJ.tsv │ ├── Pt11_on_aaCDR3perVJ.tsv │ ├── Pt11_pre_aaCDR3perVJ.tsv │ ├── Pt17_on_aaCDR3perVJ.tsv │ ├── Pt17_pre_aaCDR3perVJ.tsv │ ├── Pt18_on_aaCDR3perVJ.tsv │ ├── Pt18_pre_aaCDR3perVJ.tsv │ ├── Pt23_on_aaCDR3perVJ.tsv │ ├── Pt23_pre_aaCDR3perVJ.tsv │ ├── Pt26_on_aaCDR3perVJ.tsv │ ├── Pt26_pre_aaCDR3perVJ.tsv │ ├── Pt27_on_aaCDR3perVJ.tsv │ ├── Pt27_pre_aaCDR3perVJ.tsv │ ├── Pt28_on_aaCDR3perVJ.tsv │ ├── Pt28_pre_aaCDR3perVJ.tsv │ ├── Pt30_on_aaCDR3perVJ.tsv │ ├── Pt30_pre_aaCDR3perVJ.tsv │ ├── Pt31_on_aaCDR3perVJ.tsv │ ├── Pt31_pre_aaCDR3perVJ.tsv │ ├── Pt34_on_aaCDR3perVJ.tsv │ ├── Pt34_pre_aaCDR3perVJ.tsv │ ├── Pt37_on_aaCDR3perVJ.tsv │ ├── Pt37_pre_aaCDR3perVJ.tsv │ ├── Pt3_on_aaCDR3perVJ.tsv │ ├── Pt3_pre_aaCDR3perVJ.tsv │ ├── Pt44_on_aaCDR3perVJ.tsv │ ├── Pt44_pre_aaCDR3perVJ.tsv │ ├── Pt47_on_aaCDR3perVJ.tsv │ ├── Pt47_pre_aaCDR3perVJ.tsv │ ├── Pt48_on_aaCDR3perVJ.tsv │ ├── Pt48_pre_aaCDR3perVJ.tsv │ ├── Pt52_on_aaCDR3perVJ.tsv │ ├── Pt52_pre_aaCDR3perVJ.tsv │ ├── Pt59_on_aaCDR3perVJ.tsv │ ├── Pt59_pre_aaCDR3perVJ.tsv │ ├── Pt5_on_aaCDR3perVJ.tsv │ ├── Pt5_pre_aaCDR3perVJ.tsv │ ├── Pt67_on_aaCDR3perVJ.tsv │ ├── Pt67_pre_aaCDR3perVJ.tsv │ ├── Pt70_on_aaCDR3perVJ.tsv │ ├── Pt70_pre_aaCDR3perVJ.tsv │ ├── Pt71_on_aaCDR3perVJ.tsv │ ├── Pt71_pre_aaCDR3perVJ.tsv │ ├── Pt82_on_aaCDR3perVJ.tsv │ ├── Pt82_pre_aaCDR3perVJ.tsv │ ├── Pt8_on_aaCDR3perVJ.tsv │ ├── Pt8_pre_aaCDR3perVJ.tsv │ ├── Pt9_on_aaCDR3perVJ.tsv │ ├── Pt9_pre_aaCDR3perVJ.tsv │ └── README.md ├── exome ├── .Rapp.history ├── README.md ├── baseline_analysis.r └── baseline_clonality.r ├── neoantigen depletion ├── Mut_NeoAg_Expected_vs_Observed_BMS038.csv ├── ObsvsExpt_NeoAg.R └── README.md ├── output ├── Fig1B_part1.png ├── Fig1B_part2.png ├── Fig2A_part1_pyclone.95.clonal.ci.pdf ├── Fig2A_part2_pyclone.95.clonal.relative.ci.pdf ├── Fig2A_part3_pyclone.95.selection.relative.ci.pdf ├── Fig2B_pyclone.95.ci.boxplot.pdf ├── Fig2D_pyclone.95.densities.pdf ├── Fig5B_part1.png ├── Fig5B_part2.png ├── Fig5B_part3.png ├── Fig5B_part4.png ├── Fig5C_part1.png ├── Fig5C_part2.png ├── Fig5C_part3.png ├── Fig5C_part4.png ├── MutCnt_pretheray.csv ├── README.md ├── SupFig1A.png ├── SupFig1D.png ├── SupFig1b.png 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