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 (3.21)
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] (ORCID:
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("cBioPortalData")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software, ThirdPartyClient |
| Version | 2.19.1 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 years) |
| License | AGPL-3 |
| Depends | R (>= 4.2.0), AnVIL(>= 1.7.1), MultiAssayExperiment |
| Imports | BiocBaseUtils, 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 | bioCancer, canceR |
| Imports Me | cbaf, GNOSIS |
| Suggests Me | OmicsMLRepoR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cBioPortalData_2.19.1.tar.gz |
| Windows Binary (x86_64) | cBioPortalData_2.19.1.zip |
| macOS Binary (x86_64) | cBioPortalData_2.19.1.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/cBioPortalData/ |
| Package Short Url | https://bioconductor.org/packages/cBioPortalData/ |
| Package Downloads Report | Download Stats |