├── .gitignore ├── Analysis ├── TCGA_24_manuscript_analysis.Rmd └── TCGA_24_manuscript_analysis.html ├── Analysis_datasets ├── .RData ├── .Rhistory ├── 10_14_predictions_raw │ ├── RSEM_q_log_200_f │ │ ├── REPORT.html │ │ ├── model.txt │ │ ├── parameters.txt │ │ ├── predictions.png │ │ ├── probabilities.txt │ │ ├── signature.cdt │ │ ├── signature.png │ │ └── signature_s.cdt │ ├── TPM_q_log_200_f │ │ ├── REPORT.html │ │ ├── model.txt │ │ ├── parameters.txt │ │ ├── predictions.png │ │ ├── probabilities.txt │ │ ├── signature.cdt │ │ ├── signature.png │ │ └── signature_s.cdt │ └── fpkm_q_log_200_f │ │ ├── REPORT.html │ │ ├── model.txt │ │ ├── parameters.txt │ │ ├── predictions.png │ │ ├── probabilities.txt │ │ ├── signature.cdt │ │ ├── signature.png │ │ └── signature_s.cdt ├── 5_01_predictions_raw │ ├── fpkmlog_no │ │ ├── REPORT.html │ │ ├── predictions.png │ │ ├── signature.cdt │ │ ├── signature.png │ │ └── signature_s.cdt │ ├── rsem │ │ ├── REPORT.html │ │ ├── predictions.png │ │ ├── signature.cdt │ │ ├── signature.png │ │ └── signature_s.cdt │ ├── rsem_no │ │ ├── REPORT.html │ │ ├── predictions.png │ │ ├── signature.cdt │ │ ├── signature.png │ │ └── signature_s.cdt │ └── tpmlog_no │ │ ├── REPORT.html │ │ ├── predictions.png │ │ ├── signature.cdt │ │ ├── signature.png │ │ └── signature_s.cdt ├── Classification_12_LUAD_LUSC_Predictions.txt ├── Classification_20_LUAD_LUSC_Predictions.txt ├── GFP18_HER2_Rsubread_FPKM.txt ├── GFP18_HER2_Rsubread_TPM.txt ├── GFP18_HER2_Rsubread_geneCounts.txt ├── GFP18_HER2_TCGA_Pipeline_Expected_Gene_Counts.txt ├── GFP18_HER2_TCGA_Pipeline_Normalized_Genes_Results.txt ├── PANCAN12_19583_by_3380_numZeroes.txt ├── PANCAN20_19583_by_3380_numZeroes.txt ├── Rsem_10_14.txt ├── TCGA20_clinical_data_ordered_all_clinical_variables_samples_as_columns.txt └── rsubread_10_14.txt ├── Codes ├── BuildMatrixFile.py ├── CalcAUC.R ├── CalcAccuracy.R ├── Classify_luad_vs_lusc.R ├── CombineScalarValues.py ├── FileContainsText.py ├── GetFileExtension.py ├── IdentifyDiscordantPredictions.R ├── IdentifyInconsistentPredictions.R ├── LUSC_vs_LUAD.R ├── ParseCgHubQueryResults.py ├── ParseSampleTypes.py ├── PeekMatrix.py ├── PlotDiscordant.R ├── PrintMatrixDimensions.py ├── ProcessClinicalData.R ├── ProcessRnaSeqFeatureCounts.R ├── Split.py ├── TransposeData.py ├── biological_rep.R ├── numZero.R └── utilities.py ├── LICENSE ├── README.md ├── Scripts ├── LUSC_LUAD_discordant_analysis ├── normalize_tcga_rsubread ├── process_tcga_level_3 ├── process_tcga_rsubread └── summarize_tcga_rsubread ├── TCGA_CancerType_Abbreviations.txt └── TCGA_CancerType_Publishable.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/srp33/TCGA_RNASeq_Clinical/HEAD/.gitignore -------------------------------------------------------------------------------- /Analysis/TCGA_24_manuscript_analysis.Rmd: -------------------------------------------------------------------------------- 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