cBioPortalData
Bioc currentExposes and Makes Available Data from the cBioPortal Web Resources
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
88 28 exported
Complexity
2.7 avg / 9 max
Call network
88 nodes / 107 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
4,171
Files
46
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
28
Internal functions
57
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
19%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
AGPL-3
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-08-26
Latest release
2026-04-28
Avg cadence
153 days
Cold removal rate
100%
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 6
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 0% with a bibliography file
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/waldronlab/cbioportaldata on 2026-10-18.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| metadata_table | data.frame | 213 × 10 | No other package |
Topics
Depended on by (6)
Suggested by (1)
People
- Marcel Ramos author maintainer
- Karim Mezhoud contributor
- Levi Waldron author
Cite
Cite this package
Run in R for the authors' entry:
citation("cBioPortalData")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1200/cci.19.00119.
The repository also keeps a CITATION.cff.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.