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| TCGAutils-package | TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data |
| barcodeToUUID | Translate study identifiers from barcode to UUID and vice versa |
| builds | Utilities for working with build numbers |
| clinicalNames | Clinical dataset names in TCGA |
| CpGtoRanges | Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment |
| curatedTCGAData-helpers | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
| diseaseCodes | TCGA Cancer Disease Codes Table |
| extractBuild | Utilities for working with build numbers |
| filenameToBarcode | 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 |
| getFileName | 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 |
| imputeAssay | This function imputes assays values inside a 'MultiAssayExperiment' |
| 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 |
| mirToRanges | Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment |
| oncoPrintTCGA | OncoPrint for TCGA Mutation Assays |
| qreduceTCGA | Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment |
| sampleTables | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
| sampleTypes | Barcode Sample Type Table |
| simplifyTCGA | Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment |
| splitAssays | Helper functions for managing MultiAssayExperiment from curatedTCGAData |
| symbolsToRanges | Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment |
| TCGAbarcode | Parse data from TCGA barcode |
| TCGAbiospec | Extract biospecimen data from the TCGA barcode |
| TCGAprimaryTumors | Select primary tumors from TCGA datasets |
| TCGAsampleSelect | Select samples from barcodes from lookup table |
| TCGAutils | TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data |
| translateBuild | Utilities for working with build numbers |
| trimColData | Minimize the number of variables in colData |
| uniformBuilds | Utilities for working with build numbers |
| UUIDtoBarcode | Translate study identifiers from barcode to UUID and vice versa |
| UUIDtoUUID | Translate study identifiers from barcode to UUID and vice versa |