pathMED
Bioc currentScoring Personalized Molecular Portraits
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
PathMED is a collection of tools to facilitate precision medicine studies with omics data (e.g. transcriptomics). Among its funcionalities, genesets scores for individual samples may be calculated with several methods. These scores may be used to train machine learning models and to predict clinical features on new data. For this, several machine learning methods are evaluated in order to select the best method based on internal validation and to tune the hyperparameters. Performance metrics and a ready-to-use model to predict the outcomes for new patients are returned.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
37 10 exported
Complexity
6.4 avg / 40 max
Call network
37 nodes / 30 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
4,648
Files
46
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
26
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
33.3%
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
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-05-27
Latest release
2026-04-28
Avg cadence
168 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
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- References docs
- 71%
Topics
People
- Jordi Martorell-Marugán maintainer author
- Iván Ellson author
- Raúl López-Domínguez author
- Daniel Toro-Domínguez author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("pathMED")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.