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common_scripts
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preprocessing
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.gitattributes
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Fig1C_AML_cytscore_flow_RNAseq_comparison.R
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Fig1_plots.R
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Fig2_microenvironment_analysis.R
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Fig3A_DLBCL_cytscore_oncoprint.R
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Fig3BC_DLBCL_cytscore_boxplots.R
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Fig3D_TCGA_AML_cytscore_oncoprint.R
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Fig3_FigS3_MDSsignature.R
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Fig3_plots_scRNA.R
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Fig4D_TCGA_AML_complexheatmap_CIITA.R
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Fig5A_ligands_heatmap.R
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Fig5C_TCGA_AML_ligand_correlation_volcanoplot.R
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Fig5D_S5G_DLBCL_GSE98588_ligand_boxplots.R
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Fig5E_PDL1_IHC_boxplot.R
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Fig5F_VISTA_IHC_boxplot.R
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Fig5G_CD70_CRISPR_T cell_stimulation.R
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Fig5_DE_analysis_costim.R
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Fig6B_S6F_CGA_tSNEplot_hemap.R
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Fig6C_S6B_CGA_Hemap.R
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Fig6D_CCLE_CGA_heatmap.R
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Fig6D_CCLE_CGA_methylation.R
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Fig6F_CoMMpass_CGA_boxplot.R
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Fig6G_CoMMpass_CGA_oncoprint.R
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Fig6H_DLBCL_GSE98588_CGA_oncoprint.R
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Fig6H_FigS6H_CGA_heatmap_GSE98588.R
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Fig7_Univariate_Coxph_survival.R
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Fig7_multivariable_regression_eNet_survival.R
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Fig7_univariate_survival_forestplot.R
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FigS2AB_microenvironment_analysis_GSEA_GSVA.R
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FigS2DE_microenvironment_validation_CLL_AML.R
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FigS3L.R
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FigS4C_AML_HLAIIscore_flow_RNAseq_comparison.R
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FigS4D_TCGA_AML_global_hypermethylation.R
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FigS4EF_CIITA_methylation_validation_ERRBS.R
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FigS4J_CIITA_methylation_validation_GSE49031.R
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FigS4K_CCLE_CIITA_methylation.R
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FigS5C.R
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FigS5DE_TCGA_ligand_methylation_AML_DLBCL_comparison.R
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FigS6A_GTEx_CGA_heatmap.R
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FigS6C_Hemap_CGA_dotplots.R
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FigS6D_TCGA_antigen_methylation.R
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FigS6E_CoMMpass_CGA_heatmap.R
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FigS6G_CGA_GSEA_hemapMM.R
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README.md
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Statistical_analysis_CGA_discovery_Hemap.R
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Statistical_analysis_Cytolytic_Score_development.R
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Statistical_analysis_DE_analysis_MDSlike.R
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Statistical_analysis_FIMM_AML_RRBS.R
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Statistical_analysis_HLAII_Score_development.R
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Statistical_analysis_Szabo_TCell_analysis.R
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Statistical_analysis_Yang_NKCell_analysis.R
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Statistical_analysis_correlations_BeatAML.R
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Statistical_analysis_correlations_CoMMpass.R
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Statistical_analysis_correlations_GSE98588_DLBCL.R
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Statistical_analysis_correlations_Reddy.R
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Statistical_analysis_correlations_TCGA_AML.R
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Statistical_analysis_correlations_TCGA_DLBCL.R
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Statistical_analysis_scRNA_MDSlike_analysis.R
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datasets_synapseID.txt
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synapseID_Filename.txt
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Datasets
Models
