cBioPortalData
This is the released version of cBioPortalData; for the devel version, see cBioPortalData.
Exposes and Makes Available Data from the cBioPortal Web Resources
Bioconductor version: Release (3.23)
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 sph.cuny.edu>
citation("cBioPortalData")):Levi Waldron, Marcel Ramos. cBioPortalData: Exposes and Makes Available Data from the cBioPortal Web Resources. doi:10.18129/B9.bioc.cBioPortalData, R package version 2.24.0, https://bioconductor.org/packages/cBioPortalData.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| cBioPortalData User Guide | HTML | R Script |
| cBioPortal Data Build Errors | HTML | R Script |
| cBioPortal Developer Guide | HTML | R Script |
| cgdsr to cBioPortalData Migration | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software, ThirdPartyClient |
| Version | 2.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | AGPL-3 |
| Depends | R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment |
| Imports | BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, Seqinfo, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils |
| System Requirements | |
| URL | https://github.com/waldronlab/cBioPortalData |
| Bug Reports | https://github.com/waldronlab/cBioPortalData/issues |
See More
| Suggests | BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | bioCancer, canceR |
| Imports Me | cbaf, GNOSIS |
| Suggests Me | OmicsMLRepoR |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cBioPortalData_2.24.0.tar.gz |
| Windows Binary (x86_64) | cBioPortalData_2.24.0.zip |
| macOS Binary (big-sur-x86_64) | cBioPortalData_2.24.0.tgz |
| macOS Binary (sonoma-arm64) | cBioPortalData_2.24.0.tgz |
| 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 |