BiocOncoTK

DOI: 10.18129/B9.bioc.BiocOncoTK    

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

Bioconductor components for general cancer genomics

Bioconductor version: Development (3.11)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.7.0
In Bioconductor since BioC 3.7 (R-3.5) (1.5 years)
License Artistic-2.0
Depends R (>= 3.6.0), methods
Imports ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, utils, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures, curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz
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
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_1.7.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) BiocOncoTK_1.7.0.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 https://bioconductor.org/packages/BiocOncoTK/
Package Downloads Report Download Stats

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