BiocOncoTK

DOI: 10.18129/B9.bioc.BiocOncoTK    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see BiocOncoTK.

Bioconductor components for general cancer genomics

Bioconductor version: 3.8

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 "3.5") and enter:

if (!requireNamespace("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
PDF		Reference Manual

Details

biocViews	CopyNumberVariation, CpGIsland, DNAMethylation, GeneExpression, GeneticVariability, ImmunoOncology, SNP, Software, Transcription
Version	1.2.1
In Bioconductor since	BioC 3.7 (R-3.5) (1 year)
License	Artistic-2.0
Depends	R (>= 3.5.0), methods
Imports	ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, utils, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures
LinkingTo
Suggests	knitr, dbplyr, DBI, 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
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_1.2.1.tar.gz
Windows Binary	BiocOncoTK_1.2.1.zip
Mac OS X 10.11 (El Capitan)	BiocOncoTK_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocOncoTK
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocOncoTK
Package Short Url	http://bioconductor.org/packages/BiocOncoTK/
Package Downloads Report	Download Stats