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Bioconductor components for general cancer genomics

Bioconductor version: Release (3.19)

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))


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


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews CopyNumberVariation, CpGIsland, DNAMethylation, GeneExpression, GeneticVariability, ImmunoOncology, SNP, Software, Transcription
Version 1.24.0
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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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BiocOncoTK_1.24.0.tar.gz
Windows Binary
macOS Binary (x86_64) BiocOncoTK_1.24.0.tgz
macOS Binary (arm64) BiocOncoTK_1.24.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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