cBioPortalData

DOI: 10.18129/B9.bioc.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 (3.16)

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>

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

Installation

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

 

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 2.9.11
In Bioconductor since BioC 3.11 (R-4.0) (2.5 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_2.9.11.tar.gz
Windows Binary cBioPortalData_2.9.11.zip
macOS Binary (x86_64) cBioPortalData_2.9.11.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
Package Short Url https://bioconductor.org/packages/cBioPortalData/
Package Downloads Report Download Stats

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