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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of BiocOncoTK; for the stable release version, see BiocOncoTK.

Bioconductor components for general cancer genomics

Bioconductor version: Development (3.20)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews CopyNumberVariation, CpGIsland, DNAMethylation, GeneExpression, GeneticVariability, ImmunoOncology, SNP, Software, Transcription
Version 1.25.1
In Bioconductor since BioC 3.7 (R-3.5) (6 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, MASS, grDevices
System Requirements
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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, AnnotationHub
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