├── .gitignore ├── CELLX_analysis.Rmd ├── LICENSE ├── PAM50_EA_AA.Rmd ├── PPI_Networks.Rmd ├── README.md ├── Supplemental_R_script_1.R ├── TCGA_CNV.Rmd ├── TCGA_DEGs.Rmd ├── TCGA_DEGs_clin_subcategories.Rmd ├── TCGA_correlations.Rmd ├── TCGA_correlations_BRCA.Rmd ├── TCGA_expression.Rmd ├── TCGA_stemness.Rmd ├── TCGA_summary.Rmd ├── TCGAsurvival.Rproj ├── TCPA_correlation.Rmd ├── TNMplot.Rmd ├── TNMplot_miRNA.Rmd ├── correlations_one_vs_one.Rmd ├── data.TCGA ├── BRCA_XENA_clinical.csv ├── BRCA_with_TP53_mutation.tsv ├── CCLE_Cell_lines_annotations_20181226.txt ├── CCR-13-0583tab1.xlsx ├── Immune_resistant_program.xlsx ├── Lehmann_2019_Data1_BRCA_subtypes.xlsx ├── Lehmann_2019_Data2_TNBCsubtype.xlsx ├── PAM50_classification.txt ├── TCGA.bib ├── TCGA_489_UE.k4.txt ├── TCGA_Ancestry.xlsx ├── TCGA_cancer_counts.csv ├── TCGA_cancers.xlsx ├── TCGA_genes.txt ├── TCGA_purity.xlsx ├── TCGA_stemness.xlsx ├── TCPA_proteins.txt ├── XENA_classification.csv └── patientsAll.tsv ├── data ├── CancerDataChecklist_AppendixA.PDF ├── ClinicalVariables_AppendixC.PDF ├── DataPlatforms_AppendixB.PDF └── survplot_0.0.7.tar.gz ├── examples ├── CELLX_analysis.pdf ├── PAM50_EA_AA.pdf ├── Results_MIA_BRCA.xlsx ├── TCGA_CNV.pdf ├── TCGA_DEGs_MIA.pdf ├── TCGA_DEGs_MIA.xlsx ├── TCGA_correlations_MIA.pdf ├── TCGA_expression.pdf ├── TCGA_stemness.pdf ├── TCGA_summary.pdf ├── TNMplot.pdf ├── TNMplot_miRNA.pdf └── hsa05217.MIA.png ├── misc ├── PCA.R ├── RTCGA.R ├── TCGA_preprocessing.R ├── XENA_BRCA.R ├── aracne_networks.R ├── calcTPM.R ├── calc_feature_length.R ├── cgdsr.R ├── cgdsr_preprocessing.R ├── clinical_annotation_merge_BRCA.R ├── featureCounts2TPM.Rmd ├── overlap_significance.R └── survplot_0.0.7.tar.gz ├── styles.doc ├── NIH_grant_style.docx └── NSF_grant_style.docx ├── styles.ref └── genomebiology.csl ├── survival.Rmd └── survival_Neuroblastoma.Rmd /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/.gitignore -------------------------------------------------------------------------------- /CELLX_analysis.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/CELLX_analysis.Rmd -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/LICENSE -------------------------------------------------------------------------------- /PAM50_EA_AA.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/PAM50_EA_AA.Rmd -------------------------------------------------------------------------------- /PPI_Networks.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/PPI_Networks.Rmd -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/README.md -------------------------------------------------------------------------------- /Supplemental_R_script_1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/Supplemental_R_script_1.R -------------------------------------------------------------------------------- /TCGA_CNV.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_CNV.Rmd -------------------------------------------------------------------------------- /TCGA_DEGs.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_DEGs.Rmd -------------------------------------------------------------------------------- /TCGA_DEGs_clin_subcategories.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_DEGs_clin_subcategories.Rmd -------------------------------------------------------------------------------- /TCGA_correlations.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_correlations.Rmd -------------------------------------------------------------------------------- /TCGA_correlations_BRCA.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_correlations_BRCA.Rmd -------------------------------------------------------------------------------- /TCGA_expression.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_expression.Rmd -------------------------------------------------------------------------------- /TCGA_stemness.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_stemness.Rmd -------------------------------------------------------------------------------- /TCGA_summary.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGA_summary.Rmd -------------------------------------------------------------------------------- /TCGAsurvival.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCGAsurvival.Rproj -------------------------------------------------------------------------------- /TCPA_correlation.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TCPA_correlation.Rmd -------------------------------------------------------------------------------- /TNMplot.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TNMplot.Rmd -------------------------------------------------------------------------------- /TNMplot_miRNA.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/TNMplot_miRNA.Rmd -------------------------------------------------------------------------------- /correlations_one_vs_one.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/correlations_one_vs_one.Rmd -------------------------------------------------------------------------------- /data.TCGA/BRCA_XENA_clinical.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/BRCA_XENA_clinical.csv -------------------------------------------------------------------------------- /data.TCGA/BRCA_with_TP53_mutation.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/BRCA_with_TP53_mutation.tsv -------------------------------------------------------------------------------- /data.TCGA/CCLE_Cell_lines_annotations_20181226.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/CCLE_Cell_lines_annotations_20181226.txt -------------------------------------------------------------------------------- /data.TCGA/CCR-13-0583tab1.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/CCR-13-0583tab1.xlsx -------------------------------------------------------------------------------- /data.TCGA/Immune_resistant_program.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/Immune_resistant_program.xlsx -------------------------------------------------------------------------------- /data.TCGA/Lehmann_2019_Data1_BRCA_subtypes.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/Lehmann_2019_Data1_BRCA_subtypes.xlsx -------------------------------------------------------------------------------- /data.TCGA/Lehmann_2019_Data2_TNBCsubtype.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/Lehmann_2019_Data2_TNBCsubtype.xlsx -------------------------------------------------------------------------------- /data.TCGA/PAM50_classification.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/PAM50_classification.txt -------------------------------------------------------------------------------- /data.TCGA/TCGA.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA.bib -------------------------------------------------------------------------------- /data.TCGA/TCGA_489_UE.k4.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA_489_UE.k4.txt -------------------------------------------------------------------------------- /data.TCGA/TCGA_Ancestry.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA_Ancestry.xlsx -------------------------------------------------------------------------------- /data.TCGA/TCGA_cancer_counts.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA_cancer_counts.csv -------------------------------------------------------------------------------- /data.TCGA/TCGA_cancers.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA_cancers.xlsx -------------------------------------------------------------------------------- /data.TCGA/TCGA_genes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA_genes.txt -------------------------------------------------------------------------------- /data.TCGA/TCGA_purity.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA_purity.xlsx -------------------------------------------------------------------------------- /data.TCGA/TCGA_stemness.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCGA_stemness.xlsx -------------------------------------------------------------------------------- /data.TCGA/TCPA_proteins.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/TCPA_proteins.txt -------------------------------------------------------------------------------- /data.TCGA/XENA_classification.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/XENA_classification.csv -------------------------------------------------------------------------------- /data.TCGA/patientsAll.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data.TCGA/patientsAll.tsv -------------------------------------------------------------------------------- /data/CancerDataChecklist_AppendixA.PDF: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data/CancerDataChecklist_AppendixA.PDF -------------------------------------------------------------------------------- /data/ClinicalVariables_AppendixC.PDF: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data/ClinicalVariables_AppendixC.PDF -------------------------------------------------------------------------------- /data/DataPlatforms_AppendixB.PDF: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data/DataPlatforms_AppendixB.PDF -------------------------------------------------------------------------------- /data/survplot_0.0.7.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/data/survplot_0.0.7.tar.gz -------------------------------------------------------------------------------- /examples/CELLX_analysis.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/CELLX_analysis.pdf -------------------------------------------------------------------------------- /examples/PAM50_EA_AA.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/PAM50_EA_AA.pdf -------------------------------------------------------------------------------- /examples/Results_MIA_BRCA.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/Results_MIA_BRCA.xlsx -------------------------------------------------------------------------------- /examples/TCGA_CNV.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TCGA_CNV.pdf -------------------------------------------------------------------------------- /examples/TCGA_DEGs_MIA.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TCGA_DEGs_MIA.pdf -------------------------------------------------------------------------------- /examples/TCGA_DEGs_MIA.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TCGA_DEGs_MIA.xlsx -------------------------------------------------------------------------------- /examples/TCGA_correlations_MIA.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TCGA_correlations_MIA.pdf -------------------------------------------------------------------------------- /examples/TCGA_expression.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TCGA_expression.pdf -------------------------------------------------------------------------------- /examples/TCGA_stemness.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TCGA_stemness.pdf -------------------------------------------------------------------------------- /examples/TCGA_summary.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TCGA_summary.pdf -------------------------------------------------------------------------------- /examples/TNMplot.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TNMplot.pdf -------------------------------------------------------------------------------- /examples/TNMplot_miRNA.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/TNMplot_miRNA.pdf -------------------------------------------------------------------------------- /examples/hsa05217.MIA.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/examples/hsa05217.MIA.png -------------------------------------------------------------------------------- /misc/PCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/PCA.R -------------------------------------------------------------------------------- /misc/RTCGA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/RTCGA.R -------------------------------------------------------------------------------- /misc/TCGA_preprocessing.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/TCGA_preprocessing.R -------------------------------------------------------------------------------- /misc/XENA_BRCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/XENA_BRCA.R -------------------------------------------------------------------------------- /misc/aracne_networks.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/aracne_networks.R -------------------------------------------------------------------------------- /misc/calcTPM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/calcTPM.R -------------------------------------------------------------------------------- /misc/calc_feature_length.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/calc_feature_length.R -------------------------------------------------------------------------------- /misc/cgdsr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/cgdsr.R -------------------------------------------------------------------------------- /misc/cgdsr_preprocessing.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/cgdsr_preprocessing.R -------------------------------------------------------------------------------- /misc/clinical_annotation_merge_BRCA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/clinical_annotation_merge_BRCA.R -------------------------------------------------------------------------------- /misc/featureCounts2TPM.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/featureCounts2TPM.Rmd -------------------------------------------------------------------------------- /misc/overlap_significance.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/overlap_significance.R -------------------------------------------------------------------------------- /misc/survplot_0.0.7.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/misc/survplot_0.0.7.tar.gz -------------------------------------------------------------------------------- /styles.doc/NIH_grant_style.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/styles.doc/NIH_grant_style.docx -------------------------------------------------------------------------------- /styles.doc/NSF_grant_style.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/styles.doc/NSF_grant_style.docx -------------------------------------------------------------------------------- /styles.ref/genomebiology.csl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/styles.ref/genomebiology.csl -------------------------------------------------------------------------------- /survival.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/survival.Rmd -------------------------------------------------------------------------------- /survival_Neuroblastoma.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/TCGAsurvival/HEAD/survival_Neuroblastoma.Rmd --------------------------------------------------------------------------------