BiocOncoTK

DOI: 10.18129/B9.bioc.BiocOncoTK  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see BiocOncoTK.

Bioconductor components for general cancer genomics

Bioconductor version: 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>

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")

 

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

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
LinkingTo
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
SystemRequirements
Enhances
URL
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