markeR
Bioc currentAn R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
Release Lineage
Entered 3.22 · Oct 30, 2025
Current · Requires R 4.6
Description
markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
50 20 exported
Complexity
11.7 avg / 66 max
Call network
50 nodes / 72 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
17,106
Files
152
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
30
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.23
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
2
First release
2025-10-29
Latest release
2026-04-28
Avg cadence
181 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
- Examples that run
- 67%
- Documented parameters
- 97%
- Return-value docs
- 100%
- References docs
- 6%
Topics
People
- Rita Martins-Silva author maintainer
- Nuno Luís Barbosa-Morais author led ths
- Alexandre Kaizeler author contributor