curatedPCaData
Bioc currentCurated Prostate Cancer Data
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
9 6 exported
Complexity
6.9 avg / 25 max
Call network
9 nodes / 4 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
3,708
Files
48
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
3
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
CC BY 4.0
License flags
SPDX valid, not OSI
History
Versions
5
First release
2024-10-01
Latest release
2026-04-28
Avg cadence
175 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 27 (1 internal)includes a package overview page
- Examples that run
- 100%26 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 59%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/syksy/curatedpcadata on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| metadata | data.frame | 184 × 17 | No other package |
| template_prad | data.frame | 68 × 6 | No other package |
1 internal object is bundled for the package's own use and not listed here.
Topics
People
- Teemu Daniel Laajala author maintainer
- Federico Calboli contributor
- Christelle Colin Leitzinger contributor
- Jordan Creed contributor
- Anni Halkola contributor
- Michael Orman contributor
- Kalaimathy Singaravelu contributor
- Alex Soupir contributor
- Varsha Sreekanth contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("curatedPCaData")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41597-023-02335-4.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.