TCGAutils-package | TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data |
barcodeToUUID | Translate study identifiers from barcode to UUID and vice versa |
clinicalNames | Clinical dataset names in TCGA |
curatedTCGAData-helpers | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
diseaseCodes | TCGA Cancer Disease Codes Table |
extractBuild | Translate study identifiers from barcode to UUID and vice versa |
findGRangesCols | Obtain minimum necessary names for the creation of a GRangesList object |
generateMap | Create a sampleMap from an experiment list and phenoData dataframe |
getClinicalNames | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
getFileNames | Find the file names used in RTCGAToolbox |
getSubtypeMap | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
ID-translation | Translate study identifiers from barcode to UUID and vice versa |
makeGRangesListFromCopyNumber | Make a GRangesList from TCGA Copy Number data |
makeGRangesListFromExonFiles | Read Exon level files and create a GRangesList |
makeSummarizedExperimentFromGISTIC | Create a SummarizedExperiment from FireHose GISTIC |
mergeColData | Take a MultiAssayExperiment and include curated variables |
sampleTables | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
sampleTypes | Barcode Sample Type Table |
splitAssays | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
TCGAbarcode | Parse data from TCGA barcode |
TCGAbiospec | Extract biospecimen data from the TCGA barcode |
TCGAsampleSelect | Select samples from barcodes from lookup table |
TCGAutils | TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data |
translateBuild | Translate study identifiers from barcode to UUID and vice versa |
UUIDtoBarcode | Translate study identifiers from barcode to UUID and vice versa |