├── .DS_Store ├── .gitignore ├── 2015-TCGA-ccRCC-5-miRNAs-signatures.pdf ├── GDC ├── TCGA.KIRC.mutect.somatic.maf.gz ├── gdc_manifest.2018-08-05-LUAD-miRNA-isoform.txt ├── gdc_manifest.2018-08-05-LUAD-miRNA-seq.txt └── gdc_manifest.2018-08-05-clinical.txt ├── KIRC.Rproj ├── PPT-TCGA-ccRCC.pdf ├── Rdata ├── .DS_Store ├── KIRC-UCSC-XENA │ ├── KIRC_clinicalMatrix.gz │ ├── miRNA_GA_gene.gz │ └── miRNA_HiSeq_gene.gz ├── KIRC-broad-firehose │ ├── KIRC-FFPE │ │ ├── MANIFEST.txt │ │ └── expr.txt │ ├── KIRC │ │ ├── MANIFEST.txt │ │ └── expr.txt │ ├── clinical │ │ ├── KIRC.clin.merged.txt │ │ ├── KIRC.merged_only_biospecimen_clin_format.txt │ │ ├── KIRC.merged_only_clinical_clin_format.txt │ │ ├── KIRC.merged_only_omf_clin_format.txt │ │ └── MANIFEST.txt │ ├── gdac.broadinstitute.org_KIRC-FFPE.Merge_mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2016012800.0.0.tar.gz │ ├── gdac.broadinstitute.org_KIRC.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz │ ├── gdac.broadinstitute.org_KIRC.Merge_Clinical.Level_1.2016012800.0.0.tar.gz │ └── gdac.broadinstitute.org_KIRC.Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2016012800.0.0.tar.gz ├── TCGA-KIRC-miRNA-DEG_results.Rdata ├── TCGA-KIRC-miRNA-DESeq2-dds.Rdata ├── TCGA-KIRC-miRNA-example.Rdata ├── TCGA-KIRC-miRNA-survival_input.Rdata ├── TCGA-KIRC-miRNA-survival_results.Rdata ├── TCGA-LUAD-miRNA-example.Rdata ├── TCGA-LUAD-phe_clinical_tables.Rdata ├── TCGA-LUAD-phe_clinical_tables1.csv ├── TCGA-LUAD-phe_clinical_tables1.html ├── TCGA-LUAD-survival_input.Rdata ├── TCGA-UVM.htseq_counts.tsv.gz ├── TCGA_KIRC_miRNA_rf_output.Rdata ├── TCGA_KIRC_mut.Rdata ├── surviva.Rdata └── survival_input.Rdata ├── downloads └── brca_male_xena_vs_gdc │ ├── GDC │ ├── 0077ddf1-c0ed-485e-87b2-a7f3a7133a86 │ │ └── dfe06359-c16a-4959-bb04-298f18474a17.htseq.counts.gz │ ├── 00a9fc98-9f19-4a73-ae62-048fd7923b66 │ │ └── e30e547e-eeff-4a1f-829b-b6ec9e79f02a.htseq.counts.gz │ ├── 0c00a19b-435a-4744-b142-feb64722abc1 │ │ └── d998e259-4ea6-428d-8c47-4bc4656dbaa7.htseq.counts.gz │ ├── 50a55f2d-2edc-47eb-b6de-16d467b11d04 │ │ └── 0cb461ea-1a40-4f29-97d8-9337a74bc6c7.htseq.counts.gz │ ├── 6ec1d9a1-6c71-481c-ae53-a09c1c895029 │ │ └── fcdaa827-e263-46e0-8a83-206fa5a009ba.htseq.counts.gz │ ├── 70702a9c-a74f-4703-9dd5-24a124ebc2d5 │ │ └── f6b9d070-6d11-40f3-9ca0-a20779091825.htseq.counts.gz │ ├── 7a937bcc-decb-41e6-88e3-c50f21c34773 │ │ └── 6068fbcf-7836-41f6-8cd2-4cffde58d00a.htseq.counts.gz │ ├── 866cabeb-a740-4ba3-a680-dcface1fbafc │ │ └── b40a318f-fc61-49e5-ab41-c2e41510a12c.htseq.counts.gz │ ├── ac333fd4-b9ac-4861-b994-152c765068b3 │ │ └── 1414d172-710a-4fb6-af82-f8b0c923b259.htseq.counts.gz │ ├── c646e624-136a-4a5a-a11d-a47c3a398751 │ │ └── 06a8ba43-c1e0-4de1-9073-4b16c95245ca.htseq.counts.gz │ ├── c7741a5b-70b8-41ad-87ea-10270d2c747d │ │ └── 1a33a98d-2df8-4c2d-8042-5d2add5ce54c.htseq.counts.gz │ ├── c9f65b52-9aae-4105-a53c-7018abebde66 │ │ └── f5aa7410-7a2e-4267-ba3a-2a6a391f6b45.htseq.counts.gz │ └── e7e698aa-f2ee-4ef0-9f25-3a30a20f1d75 │ │ └── 9838a921-f1fc-434a-abe3-d396e32c32b5.htseq.counts.gz │ ├── brca_male.Rdata │ ├── brca_male.Rproj │ ├── brca_male.csv │ ├── clinical.cases_selection.2018-11-14.tar.gz │ ├── clinical.tsv │ ├── exposure.tsv │ ├── files.2018-11-14.json │ ├── from_GDC.R │ ├── from_xena.R │ ├── gdc_manifest.2018-11-14.txt │ ├── readme.md │ └── repository-files-table.2018-11-14.tsv ├── figures ├── .DS_Store ├── DEseq2_DEG_top50_pca.png ├── DEseq2_need_DEG_top50_heatmap.png ├── DEseq2_volcano.png ├── TMB_TCGA_KIRC.png ├── Vaf_TCGA_KIRC.png ├── cox_genes.heatmap.png ├── cox_genes.pca.png ├── edgeR_DEG_top50_pca.png ├── edgeR_need_DEG_top50_heatmap.png ├── edgeR_volcano.png ├── lasso_genes.heatmap.png ├── lasso_genes.pca.png ├── limma_DEG_top50_pca.png ├── limma_need_DEG_top50_heatmap.png ├── limma_volcano.png ├── logRank_genes.heatmap.png ├── logRank_genes.pca.png ├── oncoplot_top30_TCGA_KIRC.png ├── oncoplot_top30_TCGA_KIRC_noOrder.png ├── plotmafSummary_TCGA_KIRC.png ├── rf_genes.heatmap.png └── rf_genes.pca.png ├── functions.R ├── human_geneInfo_genecode_v25.rda ├── lusc_GDC_example ├── lusc_data_from_GDC.zip ├── process │ ├── gdc_manifest.tcga-lusc-clinical.txt │ ├── gdc_manifest.tcga-lusc-miRNA.txt │ ├── step1-gdc-dataset.R │ ├── tcga-lusc-clinical.json │ ├── tcga-lusc-miRNA.json │ ├── tcga-lusc.Rproj │ └── tcga_lusc_gdc_miRNA-clinical.Rdata ├── tcga-lusc-clinical-gdc.png ├── tcga-lusc-miRNA-gdc.png └── tcga-project-home.png ├── main.R ├── myTable.csv ├── readme.md ├── scripts ├── .DS_Store ├── data_for_boxplot.Rdata ├── for_scatter.Rdata ├── rf_genes.heatmap.png ├── rf_genes.pca.png ├── step00-install-packages.R ├── step01-getData-from-GDC.R ├── step01-getData-from-RTCGA.R ├── step01-getData-from-Xena.R ├── step01-getData-from-firehose.R ├── step02-DEG-3-packages.R ├── step03-batch-logRank.R ├── step04-batch-coxp.R ├── step05-lasso.R ├── step06-coxph-forest.R ├── 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