├── LICENSE ├── README.md └── TCGA-Assembler ├── Manual.pdf ├── ManualExampleData └── RawData.Firehose │ ├── READ.RPPA_AnnotateWithGene.txt │ ├── READ.methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt │ ├── READ.methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt │ ├── READ.mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.data.txt │ ├── READ.rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data.data.txt │ └── READ.snp__genome_wide_snp_6__broad_mit_edu__hg18__Level_3__segmented_scna_hg18__seg.seg.txt ├── Module_A.R ├── Module_B.R ├── QuickStartExample.R ├── SupportingFiles ├── Hg18GenePosition.txt ├── Hg19GenePosition.txt ├── MethylationChipAnnotation.rda └── TCGASampleType.txt ├── Tutorial.pdf └── curl.exe /LICENSE: -------------------------------------------------------------------------------- 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