BiocOncoTK

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BiocOncoTK.

Bioconductor components for general cancer genomics


Bioconductor version: 3.13

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 "4.1") 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 1.12.1
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
System Requirements
URL
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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
Linking To
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Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package BiocOncoTK_1.12.1.tar.gz
Windows Binary BiocOncoTK_1.12.1.zip
macOS 10.13 (High Sierra) BiocOncoTK_1.12.1.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
Old Source Packages for BioC 3.13 Source Archive