├── .DS_Store ├── .gitignore ├── brca_metabric ├── .DS_Store ├── LICENSE ├── case_lists │ ├── cases_nat_comm_2016.txt │ └── cases_nature_2012.txt ├── data_clinical_patient.txt ├── data_clinical_sample.txt ├── data_gene_matrix.txt ├── data_gene_panel.txt ├── data_mutations_extended.txt ├── meta_CNA.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_expression.txt ├── meta_gene_matrix.txt ├── meta_mutations_extended.txt ├── meta_study.txt ├── validation_error_file.txt └── validation_report.html ├── data ├── metabric_CNA.Rdata ├── metabric_clinical.Rdata ├── metabric_expression.Rdata ├── metabric_mut_positions.Rdata ├── metabric_mutations.Rdata ├── metebric_mut_freq.Rdata └── metebric_signature_output.Rdata ├── figures ├── .DS_Store ├── BRCA1_expression_by_HER2_SNP6_CNA.png ├── HER2_SNP6_CNA_by_subtype.png ├── Mutation_relations.png ├── PAM50-VS-Clinical.png ├── all_signatures.cosmic.sig.pdf ├── ht_by_pam50_raw.png ├── ht_by_pam50_scale.png ├── logRank_genes.heatmap.png ├── logRank_genes.pca.png ├── oncoplot_top30_metabric.png ├── plotmafSummary_metabric.png ├── signatures.cosmic.heatmap.png ├── survival_based_on_AHNAK2_mutation.png ├── survival_based_on_ER_IHC.png ├── survival_based_on_MUC16_mutation.png ├── survival_based_on_PIK3CA_mutation.png ├── survival_based_on_SYNE1_mutation.png └── survival_based_on_TP53_mutation.png ├── metabric.Rproj ├── re-analysis-METABRIC.pptx ├── readme.md ├── ref └── 生存分析介绍.pdf ├── scripts ├── step0-install_packages.R ├── step1-check_clinical.R ├── step2-check-expression.R ├── step3-check-CNA.R ├── step4-check-mutations.R ├── step5-mutation-signatures.R ├── step6-maftools.R ├── step7-batch-survival.R └── step8-pam50.R └── tips └── gsva_sur ├── geneSets.gmt ├── gsva_sur.Rproj └── readme.md /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmzeng1314/METABRIC/HEAD/.DS_Store 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