This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

BiocOncoTK

Bioconductor components for general cancer genomics

Bioconductor version: Release (3.17)

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

Author: Vince Carey

Maintainer: VJ Carey <stvjc at channing.harvard.edu>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocOncoTK")

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

Documentation

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

browseVignettes("BiocOncoTK")
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

Details

biocViews CopyNumberVariation, CpGIsland, DNAMethylation, GeneExpression, GeneticVariability, ImmunoOncology, SNP, Software, Transcription
Version 1.20.0
In Bioconductor since BioC 3.7 (R-3.5) (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, MASS, grDevices
Linking To
Suggests knitr, dbplyr, org.Hs.eg.db, 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
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package BiocOncoTK_1.20.0.tar.gz
Windows Binary BiocOncoTK_1.20.0.zip
macOS Binary (x86_64) BiocOncoTK_1.20.0.tgz
macOS Binary (arm64) BiocOncoTK_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocOncoTK
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocOncoTK
Bioc Package Browser https://code.bioconductor.org/browse/BiocOncoTK/
Package Short Url https://bioconductor.org/packages/BiocOncoTK/
Package Downloads Report Download Stats