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: Release (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 |
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 |
See More
| 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 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 |