cbpManager
Bioc currentGenerate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
39 2 exported
Complexity
5.4 avg / 26 max
Call network
39 nodes / 15 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
4,068
Files
165
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
28
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
AGPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-08-04
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 42includes a package overview page
- Examples that run
- 92%11 run in a plain check (1 of them under a condition) · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- intro.html HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/arsenij-ust/cbpmanager on 2026-10-22.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| predefined_patient_cols | data.frame | 22 × 4 | No other package |
| predefined_sample_cols | data.frame | 21 × 4 | No other package |
Topics
People
- Arsenij Ustjanzew author maintainer copyright holder
- Federico Marini author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cbpManager")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.