cBioPortalData

DOI: 10.18129/B9.bioc.cBioPortalData  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cBioPortalData.

Exposes and makes available data from the cBioPortal web resources

Bioconductor version: 3.16

The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.

Author: Levi Waldron [aut], Marcel Ramos [aut, cre] , Karim Mezhoud [ctb]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("cBioPortalData")

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("cBioPortalData")

 

HTML	R Script	cBioPortal Data Build Errors
HTML	R Script	cBioPortal Developer Guide
HTML	R Script	cBioPortalData User Guide
HTML	R Script	cgdsr to cBioPortalData Migration
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software, ThirdPartyClient
Version	2.10.3
In Bioconductor since	BioC 3.11 (R-4.0) (3 years)
License	AGPL-3
Depends	R (>= 4.2.0), AnVIL(>= 1.7.1), MultiAssayExperiment
Imports	BiocFileCache(>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox(>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils(>= 1.9.4), utils
LinkingTo
Suggests	BiocStyle, knitr, survival, survminer, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/waldronlab/cBioPortalData/issues
Depends On Me
Imports Me	cbaf, LowMACA, PrecisionTrialDrawer
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	cBioPortalData_2.10.3.tar.gz
Windows Binary	cBioPortalData_2.10.3.zip
macOS Binary (x86_64)	cBioPortalData_2.10.3.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/cBioPortalData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cBioPortalData
Bioc Package Browser	https://code.bioconductor.org/browse/cBioPortalData/
Package Short Url	https://bioconductor.org/packages/cBioPortalData/
Package Downloads Report	Download Stats