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cbioportalR: Browse and Query Clinical and Genomic Data from cBioPortal

Provides R users with direct access to genomic and clinical data from the 'cBioPortal' web resource via user-friendly functions that wrap 'cBioPortal's' existing API endpoints <https://www.cbioportal.org/api/swagger-ui/index.html>. Users can browse and query genomic data on mutations, copy number alterations and fusions, as well as data on tumor mutational burden ('TMB'), microsatellite instability status ('MSI'), 'FACETS' and select clinical data points (depending on the study). See <https://www.cbioportal.org/> and Gao et al., (2013) <doi:10.1126/scisignal.2004088> for more information on the cBioPortal web resource.

Version: 1.1.1
Depends: R (≥ 2.10)
Imports: httr (≥ 1.4.3), tibble (≥ 3.1.7), purrr (≥ 0.3.4), magrittr (≥ 2.0.3), rlang (≥ 1.0.3), glue (≥ 1.6.2), jsonlite (≥ 1.8.0), tidyr (≥ 1.2.0), dplyr (≥ 1.0.9), stringr (≥ 1.4.0), cli (≥ 3.3.0)
Suggests: testthat (≥ 3.1.4), knitr (≥ 1.39), rmarkdown (≥ 2.14), covr (≥ 3.5.1), spelling
Published: 2024-11-20
DOI: 10.32614/CRAN.package.cbioportalR
Author: Karissa Whiting ORCID iD [aut, cre, cph]
Maintainer: Karissa Whiting <karissa.whiting at gmail.com>
BugReports: https://github.com/karissawhiting/cbioportalR/issues
License: MIT + file LICENSE
URL: https://github.com/karissawhiting/cbioportalR, https://www.karissawhiting.com/cbioportalR/
NeedsCompilation: no
Language: en-US
Materials: README NEWS
In views: Omics
CRAN checks: cbioportalR results

Documentation:

Reference manual: cbioportalR.pdf
Vignettes: Internal Structure & Guiding Principles (source, R code)
Overview of Data Retrieval Workflow (source)

Downloads:

Package source: cbioportalR_1.1.1.tar.gz
Windows binaries: r-devel: cbioportalR_1.1.1.zip, r-release: cbioportalR_1.1.1.zip, r-oldrel: cbioportalR_1.1.1.zip
macOS binaries: r-release (arm64): cbioportalR_1.1.1.tgz, r-oldrel (arm64): cbioportalR_1.1.1.tgz, r-release (x86_64): cbioportalR_1.1.1.tgz, r-oldrel (x86_64): cbioportalR_1.1.1.tgz
Old sources: cbioportalR archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.