vignettes/curatedTCGAData_ref.Rmd
curatedTCGAData_ref.RmdTCGAutils::diseaseCodes
| Study.Abbreviation | Available | SubtypeData | Study.Name |
|---|---|---|---|
| ACC | Yes | Yes | Adrenocortical carcinoma |
| BLCA | Yes | Yes | Bladder Urothelial Carcinoma |
| BRCA | Yes | Yes | Breast invasive carcinoma |
| CESC | Yes | No | Cervical squamous cell carcinoma and endocervical adenocarcinoma |
| CHOL | Yes | No | Cholangiocarcinoma |
| CNTL | No | No | Controls |
| COAD | Yes | Yes | Colon adenocarcinoma |
| DLBC | Yes | No | Lymphoid Neoplasm Diffuse Large B-cell Lymphoma |
| ESCA | Yes | No | Esophageal carcinoma |
| FPPP | No | No | FFPE Pilot Phase II |
| GBM | Yes | Yes | Glioblastoma multiforme |
| HNSC | Yes | Yes | Head and Neck squamous cell carcinoma |
| KICH | Yes | Yes | Kidney Chromophobe |
| KIRC | Yes | Yes | Kidney renal clear cell carcinoma |
| KIRP | Yes | Yes | Kidney renal papillary cell carcinoma |
| LAML | Yes | Yes | Acute Myeloid Leukemia |
| LCML | No | No | Chronic Myelogenous Leukemia |
| LGG | Yes | Yes | Brain Lower Grade Glioma |
| LIHC | Yes | No | Liver hepatocellular carcinoma |
| LUAD | Yes | Yes | Lung adenocarcinoma |
| LUSC | Yes | Yes | Lung squamous cell carcinoma |
| MESO | Yes | No | Mesothelioma |
| MISC | No | No | Miscellaneous |
| OV | Yes | Yes | Ovarian serous cystadenocarcinoma |
| PAAD | Yes | No | Pancreatic adenocarcinoma |
| PCPG | Yes | No | Pheochromocytoma and Paraganglioma |
| PRAD | Yes | Yes | Prostate adenocarcinoma |
| READ | Yes | No | Rectum adenocarcinoma |
| SARC | Yes | No | Sarcoma |
| SKCM | Yes | Yes | Skin Cutaneous Melanoma |
| STAD | Yes | Yes | Stomach adenocarcinoma |
| TGCT | Yes | No | Testicular Germ Cell Tumors |
| THCA | Yes | Yes | Thyroid carcinoma |
| THYM | Yes | No | Thymoma |
| UCEC | Yes | Yes | Uterine Corpus Endometrial Carcinoma |
| UCS | Yes | No | Uterine Carcinosarcoma |
| UVM | Yes | No | Uveal Melanoma |
| ExperimentList data types | Description |
|---|---|
| SummarizedExperiment* | |
| RNASeqGene | RSEM TPM gene expression values |
| RNASeq2GeneNorm | Upper quartile normalized RSEM TPM gene expression values |
| miRNAArray | Probe-level miRNA expression values |
| miRNASeqGene | Gene-level log2 RPM miRNA expression values |
| mRNAArray | Unified gene-level mRNA expression values |
| mRNAArray_huex | Gene-level mRNA expression values from Affymetrix Human Exon Array |
| mRNAArray_TX_g4502a | Gene-level mRNA expression values from Agilent 244K Array |
| mRNAArray_TX_ht_hg_u133a | Gene-level mRNA expression values from Affymetrix Human Genome U133 Array |
| GISTIC_AllByGene | Gene-level GISTIC2 copy number values |
| GISTIC_ThresholdedByGene | Gene-level GISTIC2 thresholded discrete copy number values |
| RPPAArray | Reverse Phase Protein Array normalized protein expression values |
| RangedSummarizedExperiment | |
| GISTIC_Peaks | GISTIC2 thresholded discrete copy number values in recurrent peak regions |
| SummarizedExperiment with HDF5Array DelayedMatrix | |
| Methylation_methyl27 | Probe-level methylation beta values from Illumina HumanMethylation 27K BeadChip |
| Methylation_methyl450 | Probe-level methylation beta values from Infinium HumanMethylation 450K BeadChip |
| RaggedExperiment | |
| CNASNP | Segmented somatic Copy Number Alteration calls from SNP array |
| CNVSNP | Segmented germline Copy Number Variant calls from SNP Array |
| CNASeq | Segmented somatic Copy Number Alteration calls from low pass DNA Sequencing |
| Mutation* | Somatic mutations calls |
| CNACGH_CGH_hg_244a | Segmented somatic Copy Number Alteration calls from CGH Agilent Microarray 244A |
| CNACGH_CGH_hg_415k_g4124a | Segmented somatic Copy Number Alteration calls from CGH Agilent Microarray 415K |
| * All can be converted to RangedSummarizedExperiment (except RPPAArray) with TCGAutils | |