cBioPortalData

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see cBioPortalData.

Exposes and makes available data from the cBioPortal web resources

Bioconductor version: 3.14

The cBioPortalData package takes compressed resources from repositories such as cBioPortal and assembles a MultiAssayExperiment object with Bioconductor classes.

Author: Levi Waldron [aut], Marcel Ramos [aut, cre]

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

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

Installation

To install this package, start R (version "4.1") 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")

cBioPortal Data Build Errors HTML R Script

cBioPortal Quick-start Guide HTML R Script

cBioPortal User Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Infrastructure, Software, ThirdPartyClient

Version 2.6.1

In Bioconductor since BioC 3.11 (R-4.0) (4 years)

License AGPL-3

Depends R (>= 4.0.0), AnVIL, 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

Suggests BiocStyle, knitr, survival, survminer, rmarkdown, testthat

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 cBioPortalData_2.6.1.tar.gz

Windows Binary cBioPortalData_2.6.1.zip

macOS 10.13 (High Sierra) cBioPortalData_2.6.1.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

Old Source Packages for BioC 3.14 Source Archive