CoreGx
Bioc currentClasses and Functions to Serve as the Basis for Other 'Gx' Packages
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
201 82 exported
Complexity
3.6 avg / 75 max
Call network
201 nodes / 163 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
19,853
Files
191
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
157
Internal functions
110
Testing & CI
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
76.4%
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
4.1
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-06-09
Latest release
2026-04-28
Avg cadence
178 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 95%
- Documented parameters
- 94%
- Return-value docs
- 99%
- References docs
- 3%
Topics
Depended on by (5)
Bioconductor (5)
People
- Benjamin Haibe-Kains author maintainer
- Christopher Eeles author
- Jermiah Joseph author
- Feifei Li author
- Petr Smirnov author
- Ian Smith author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("CoreGx")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.