DOI: 10.18129/B9.bioc.TCGAutils  

TCGA utility functions for data management

Bioconductor version: Release (3.17)

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

Author: Marcel Ramos [aut, cre] , Lucas Schiffer [aut], Sean Davis [ctb], Levi Waldron [aut]

Maintainer: Marcel Ramos <marcel.ramos at>

Citation (from within R, enter citation("TCGAutils")):


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biocViews DataImport, Preprocessing, Software, WorkflowStep
Version 1.20.4
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports AnnotationDbi, BiocBaseUtils, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment(>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
Suggests AnnotationHub, BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db,, RColorBrewer, readr, rmarkdown, RTCGAToolbox(>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene
Depends On Me
Imports Me cBioPortalData, RTCGAToolbox, terraTCGAdata
Suggests Me CNVRanger, curatedTCGAData, dce, glmSparseNet, IntOMICS
Links To Me
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