GitHub - rossmacp/CM9_response: Code and data to support doi:10.1136/jitc-2020-001506

doi:10.1136/jitc-2020-001506

This release has been Approved by BMS: PubD - 00053752

This document describes the relationship of code to figures:

CM009 Manuscript Code outputs.txt

Affymetrix gene expression data and annotation are available in ArrayExpress as E-MTAB-3218.

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Name		Name	Last commit message	Last commit date
Latest commit History 27 Commits
Data		Data
10_Probeset_GeneSet_Annotation.Rmd		10_Probeset_GeneSet_Annotation.Rmd
20_Response_Analysis_Criterion.Rmd		20_Response_Analysis_Criterion.Rmd
30_Response_Analysis_Baseline.Rmd		30_Response_Analysis_Baseline.Rmd
31_CM25_AIM2plot.Rmd		31_CM25_AIM2plot.Rmd
35_GeneSetEnrichment_Response_Baseline_Day28.Rmd		35_GeneSetEnrichment_Response_Baseline_Day28.Rmd
40_Response_Analysis_Week4.Rmd		40_Response_Analysis_Week4.Rmd
50_Response_x_Time_Analysis.Rmd		50_Response_x_Time_Analysis.Rmd
51_RBM_Plot_Serum_IL18.Rmd		51_RBM_Plot_Serum_IL18.Rmd
60_TCR_analysis.Rmd		60_TCR_analysis.Rmd
70_Baseline_Tcell_analysis.Rmd		70_Baseline_Tcell_analysis.Rmd
75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd		75_GeneSetEnrichment_CD3TCRsig_Baseline_Day28.Rmd
80_Week4_Tcellhigh_NonResponder_analysis.Rmd		80_Week4_Tcellhigh_NonResponder_analysis.Rmd
90_Baseline_Genesets_ccrcc_Assignment.Rmd		90_Baseline_Genesets_ccrcc_Assignment.Rmd
95_Baseline_Genesets_ccrcc_Analyses.Rmd		95_Baseline_Genesets_ccrcc_Analyses.Rmd
96_Response_Analysis_Baseline_vs_ccrcc.Rmd		96_Response_Analysis_Baseline_vs_ccrcc.Rmd
CM009 Manuscript Code outputs.txt		CM009 Manuscript Code outputs.txt
Petras references EndnoteX.enl		Petras references EndnoteX.enl
README.md		README.md
ggplot_theme_dj_prm.R		ggplot_theme_dj_prm.R