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cBioPortalData

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

Exposes and Makes Available Data from the cBioPortal Web Resources


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("cBioPortalData")):

Installation

To install this package, start R (version "4.4") and enter:


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

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

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

Details

biocViews Infrastructure, Software, ThirdPartyClient
Version 2.15.3
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements
URL
Bug Reports https://github.com/waldronlab/cBioPortalData/issues
See More
Suggests BiocStyle, knitr, survival, survminer, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me cbaf, GNOSIS
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cBioPortalData_2.15.3.tar.gz
Windows Binary cBioPortalData_2.15.3.zip
macOS Binary (x86_64) cBioPortalData_2.15.3.tgz
macOS Binary (arm64) cBioPortalData_2.15.0.tgz
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