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CM009 Manuscript Code outputs.txt
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CM009 Manuscript Code outputs.txt
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ORDER Type Item file Script
1 Figure 1a Clinical_Heatmap_Annotation_91_Subjects_Select.pdf 20_Response_Analysis_Criterion.Rmd
2 Figure 1b Clinical_KM_PFS_85_Subjects.pdf 20_Response_Analysis_Criterion.Rmd
3 Figure 2a GEP_Heatmap_Biopsy_Screen_ResponseEffect_93genes.pdf 30_Response_Analysis_Baseline.Rmd
4 Figure 2b pathwaze_Response_baseline_Hallmark_plot.png 35_GeneSetEnrichment_Response_Baseline_Day28.Rmd
5 Figure 2c GEP_Boxplot_Response_Baseline_9447_at_AIM2.png 30_Response_Analysis_Baseline.Rmd
6 Figure 2d GEP_Boxplot_Response_OR_CM25_AIM2.png 31_CM25_AIM2plot.Rmd
7 Figure 3a GEP_Heatmap_Biopsy_Week4_ResponseEffect.pdf 40_Response_Analysis_Week4.Rmd
8 Figure 3b pathwaze_Response_day28_Hallmark_plot.png 35_GeneSetEnrichment_Response_Baseline_Day28.Rmd
9 Figure 3c GEP_Boxplot_Response_Week4_Multigene.png 40_Response_Analysis_Week4.Rmd
10 Figure 4a GEP_Heatmap_Biopsy_All_TimeResponseEffect.pdf 50_Response_x_Time_Analysis.Rmd
11 Figure 4b pathwaze_Response_time_vs_response_Hallmark_plot.png 35_GeneSetEnrichment_Response_Baseline_Day28.Rmd
12 Figure 4c GEP_Boxplot_Time_By_Response_3606_at_IL18.png 50_Response_x_Time_Analysis.Rmd
13 Figure 4d IL18_vs_C1D1_0H_C2D1_0H_ByResponse.png 51_RBM_Plot_IL18.R
14 Figure 5a TCR_baseline_clonality_response.png 60_TCR_analysis.Rmd
15 Figure 5a TCR_Change_clonality_response.png 60_TCR_analysis.Rmd
16 Figure 5b GEP_Scatterplot_CD3TCRScore_Baseline_CCL28.png 70_Baseline_Tcell_analysis.Rmd
17 Figure 5b GEP_Scatterplot_CD3TCRScore_Baseline_CA9.png 70_Baseline_Tcell_analysis.Rmd
18 Figure 5c pathwaze_CD3TCRsig_baseline_Hallmark_plot.png 75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd
19 Figure 5d GEP_Heatmap_Biopsy_Screen_CD3TCR_HIF1A.pdf 70_Baseline_Tcell_analysis.Rmd
20 Figure 5e GEP_Scatterplot_CD3TCRScore_Baseline_WntGenes.png 70_Baseline_Tcell_analysis.Rmd
21 Figure 6a GEP_Boxplot_TCRhigh_Week4_7852_at_CXCR4.png 80_Week4_Tcellhigh_NonResponder_analysis.Rmd
22 Figure 6a GEP_Boxplot_TCRhigh_Week4_958_at_CD40.png 80_Week4_Tcellhigh_NonResponder_analysis.Rmd
23 Figure 6b pathwaze_CD3TCRsigHi_Day28_Hallmark_plot.png 75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd
24 Figure 6c GEP_Heatmap_Biopsy_Week4_CD3sigHigh_IFNG_p01.pdf 80_Week4_Tcellhigh_NonResponder_analysis.Rmd
25 Figure 7a GEP_Heatmap_Signatures_Clustered_Pub_Annotation_56Subjects_Screen_Waterfall.pdf 95_Baseline_Genesets_ccrcc_Analyses.Rmd
26 Figure 7b GEP_barchart_ORR_ccrccCluster.png 95_Baseline_Genesets_ccrcc_Analyses.Rmd
27 Figure 7c GEP_Signature_Baseline_ROC_All_Pub.png 95_Baseline_Genesets_ccrcc_Analyses.Rmd
28 Figure 7d GEP_Signature_Baseline_Forest_Pub.png 95_Baseline_Genesets_ccrcc_Analyses.Rmd
29 Figure 7e GEP_Heatmap_EMTAB3267_BMS93.pdf 96_Response_Analysis_Baseline_vs_ccrcc.Rmd
30 Supplemental Figure S1 Clinical_Heatmap_Annotation_91_Subjects_All.pdf 20_Response_Analysis_Criterion.Rmd
31 Supplemental Figure S2 CM9 Patient 98 Index lesions.png 13_07 CA209 interim results LEEF LETM LEA.xlsx
32 Supplemental Figure S3 Clinical_KM_OS_85_Subjects.pdf 20_Response_Analysis_Criterion.Rmd
33 Supplemental Figure S4a Clinical_Scatterplot_MPCT_PFS_85_Subjects.png 20_Response_Analysis_Criterion.Rmd
34 Supplemental Figure S4b Clinical_Scatterplot_MPCT_PFS_56_Subjects_Baseline.png 20_Response_Analysis_Criterion.Rmd
35 Supplemental Figure S5 Taken From P01361_CA209009_Patient_and_sample_annotation P01361_CA209009_Patient_and_sample_annotation
36 Supplemental Figure S6a GEP_Heatmap_Biopsy_Screen_ResponseEffect_Cluster.pdf 30_Response_Analysis_Baseline.Rmd
37 Supplemental Figure S6b GEP_Heatmap_Biopsy_Week4_ResponseEffect_Cluster.pdf 40_Response_Analysis_Week4.Rmd
38 Supplemental Figure S7 TCR_delta_clonality_response.pdf 60_TCR_analysis.Rmd
39 Supplemental Figure S8 GEP_Heatmap_Biopsy_Screen_CD3sig_Score.pdf 70_Baseline_Tcell_analysis.Rmd
40 Supplemental Figure S9a pathwaze_CD3TCRsig_baseline_C2_plot.png 75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd
41 Supplemental Figure S9b pathwaze_CD3TCRsig_baseline_Hallmark_plot.png 75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd
42 Supplemental Figure S10a pathwaze_CD3TCRsigHi_Day28_Hallmark_plot.png 75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd
43 Supplemental Figure S10b GEP_Heatmap_Biopsy_Week4_CD3sigHigh_IFNA.pdf 80_Week4_Tcellhigh_NonResponder_analysis.Rmd
44 Supplemental Figure S10c GEP_Heatmap_Biopsy_Week4_CD3sigHigh_IFNG.pdf 80_Week4_Tcellhigh_NonResponder_analysis.Rmd
45 Supplemental Figure S11 GEP_Boxplot_Signatures_Baseline_Angio_ccrcc.png 95_Baseline_Genesets_ccrcc_Analyses.Rmd
46 Supplemental Figure S12 GEP_Signature_Baseline_ROC_Facet_Pub.png 95_Baseline_Genesets_ccrcc_Analyses.Rmd
47 Supplemental Figure S12 GEP_Table_BiopsyScreen_GEPSignatures_AUC_Odds.txt 95_Baseline_Genesets_ccrcc_Analyses.Rmd
48 Supplemental Figure S13a "CM9 48 patients: OR Percentage, By PBRM1" 95_Baseline_Genesets_ccrcc_Analyses.Rmd
49 Supplemental Figure S13b GEP_barchart_PBRM1_ccrccCluster.png 95_Baseline_Genesets_ccrcc_Analyses.Rmd
50 Supplemental Figure S14a GEP_Heatmap_EMTAB3267_BMS311.pdf 96_Response_Analysis_Baseline_vs_ccrcc.Rmd
51 Supplemental Figure S14b GEP_Boxplot_Signatures_Baseline_BMS_ccrcc.png 95_Baseline_Genesets_ccrcc_Analyses.Rmd
52 Supplemental Table S1 U219_BrainArray_2151probesets_used.txt 10_Probeset_GeneSet_Annotation.Rmd
53 Supplemental Table S2 CM9_Patient_Annotation.txt P01361_CA209009_Patient_and_sample_annotation
54 Supplemental Table S3 GEP_Table_BiopsyScreen_ResponseEffect_311prbs.txt 30_Response_Analysis_Baseline.Rmd
55 Supplemental Table S4 Ascierto Topalian list vs CM9 Ascierto Topalian list vs CM9.xlsx
56 Supplemental Table S5 GEP_Table_BiopsyWeek4_ResponseEffect_779prbs.txt 40_Response_Analysis_Week4.Rmd
57 Supplemental Table S6 GEP_Table_BiopsyAll_TimeResponseEffect_189prbs.txt 50_Response_x_Time_Analysis.Rmd
58 Supplemental Table S7 GEP_Table_BiopsyScreen_CD3sigEffect_1336prbs.txt 70_Baseline_Tcell_analysis.Rmd
59 Supplemental Table S8 GEP_Table_BiopsyScreen_CD3sigEffect_IRISsummary.txt 70_Baseline_Tcell_analysis.Rmd
60 Supplemental Table S9 GEP_Table_BiopsyScreen_CD3sigEffect_NegativeImmune_281prbs.txt 70_Baseline_Tcell_analysis.Rmd
61 Supplemental Table S10 GEP_Table_BiopsyWeek4_27samples_CD3sigHigh_18571prbs.txt 70_Baseline_Tcell_analysis.Rmd
62 Supplemental Table S11 GEP_Table_BiopsyWeek4_27samples_CD3sigHigh_P01_210prbs.txt 80_Week4_Tcellhigh_NonResponder_analysis.Rmd
63 Supplemental Table S12 derived from pathwaze_CD3TCRsigHi_Day28_Hallmark_table_detail.csv 75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd
64 Supplemental Table S13 GEP_Table_BiopsyScreen_OddsRatio_Results.txt 95_Baseline_Genesets_ccrcc_Analyses.Rmd