consensusOV
Bioc currentGene expression-based subtype classification for high-grade serous ovarian cancer
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
9 8 exported
Complexity
3 avg / 13 max
Call network
9 nodes / 6 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
1,168
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
0
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
9.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-10-30
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
- 9
- Examples that run
- 100%7 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 56%
Repository practices
4 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/bhklab/consensusov on 2026-10-25.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| FT_vs_OSE_signature | data.frame | 112 × 3 | No other package |
| GSE14764.eset | – | – | – |
5 internal objects are bundled for the package's own use and not listed here.
Topics
Depended on by (1)
Bioconductor (1)
People
- Benjamin Haibe-Kains author maintainer
- Gregory M Chen author
- Christopher Eeles contributor
- Ludwig Geistlinger author
- Lavanya Kannan author
- Victor Kofia author
- Levi Waldron author
Cite
Cite this package
Run in R for the authors' entry:
citation("consensusOV")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1158/1078-0432.ccr-18-0784.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.