BiocOncoTK

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see BiocOncoTK.

Bioconductor components for general cancer genomics


Bioconductor version: 3.19

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 "4.4") 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 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6.5 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
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, AnnotationHub
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package BiocOncoTK_1.24.0.tar.gz
Windows Binary (x86_64) BiocOncoTK_1.24.0.zip (64-bit only)
macOS Binary (x86_64) BiocOncoTK_1.24.0.tgz
macOS Binary (arm64) BiocOncoTK_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiocOncoTK
Source Repository (Developer Access) git clone [email protected]:packages/BiocOncoTK
Bioc Package Browser https://code.bioconductor.org/browse/BiocOncoTK/
Package Short Url https://bioconductor.org/packages/BiocOncoTK/
Package Downloads Report Download Stats