DOI: 10.18129/B9.bioc.BiocOncoTK  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BiocOncoTK.

Bioconductor components for general cancer genomics

Bioconductor version: 3.16

Provide a central interface to various tools for genome-scale analysis of cancer studies.

Author: Vince Carey

Maintainer: VJ Carey <stvjc at>

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


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HTML R Script BiocOncoTK -- cancer oriented components for Bioconductor
HTML R Script curatedMSIData overview
HTML R Script Mapping TCGA tumor codes to NCIT
PDF   Reference Manual


biocViews CopyNumberVariation, CpGIsland, DNAMethylation, GeneExpression, GeneticVariability, ImmunoOncology, SNP, Software, Transcription
Version 1.18.0
In Bioconductor since BioC 3.7 (R-3.5) (5 years)
License Artistic-2.0
Depends R (>= 3.6.0), methods, utils
Imports ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures, curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz
Suggests knitr, dbplyr,, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE(>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75, rmarkdown, rhdf5client
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