cBioPortalData
Exposes and Makes Available Data from the cBioPortal Web Resources
Bioconductor version: 3.23 · Package version: 2.24.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cBioPortalData")Details
| Maintainer | Marcel Ramos <marcel.ramos@sph.cuny.edu> |
| Author | Levi Waldron [aut], Marcel Ramos [aut, cre] (ORCID: <https://orcid.org/0000-0002-3242-0582>), Karim Mezhoud [ctb] |
| License | AGPL-3 |
| URL | https://github.com/waldronlab/cBioPortalData |
| Bug Reports | https://github.com/waldronlab/cBioPortalData/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Infrastructure, Software, ThirdPartyClient |
| Package Short Url | https://bioconductor.org/packages/cBioPortalData/ |
Citation
From within R, enter 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.
Documentation
- cBioPortalData: Data Build Errors
- cBioPortalData: API Reference Guide for Devs
- cBioPortalData: User Guide
- cgdsr to cBioPortalData: Migration Tutorial
Download
Follow the 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 (arm64) | cBioPortalData_2.24.0.tgz |
| macOS binary (x86_64) | cBioPortalData_2.24.0.tgz |
Dependencies
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
Suggests: BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown, testthat