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.
None published for Bioconductor
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
15,959
Files
118
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
20
Internal functions
30
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.23
testthat edition
3
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
- Help pages
- 53 (29 internal)includes a package overview page
- Examples that run
- 67%20 run in a plain check · 10 never run
- Exported functions with examples
- 100%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 6%
Repository practices
8 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/diseasetranscriptomicslab/marker on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-07-08 · The repository has a site deploy workflow
pkgdown site last built 2026-07-08
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| counts_example | data.frame | 10,373 × 39 | No other package |
| genesets_example | list | 3 elements | No other package |
| metadata_example | data.frame | 39 × 6 | No other package |
Topics
People
- Rita Martins-Silva author maintainer
- Nuno Luís Barbosa-Morais author led thesis advisor
- Alexandre Kaizeler author contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("markeR")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 v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.