pathMED
This is the released version of pathMED; for the devel version, see pathMED.
All Bioconductor versions of pathMED
3.24 (devel), 3.23 (release), 3.22, 3.21
Scoring Personalized Molecular Portraits
Bioconductor version: 3.23 · Package version: 1.4.0
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.
Author: Jordi Martorell-Marugán [cre, aut] 
, Daniel Toro-Domínguez [aut] , Raúl López-Domínguez [aut] , Iván Ellson [aut]
Maintainer: Jordi Martorell-Marugán <jmartorellm at gmail.com>
Citation
From within R, enter citation("pathMED"):
Jordi Martorell-Marugán, Daniel Toro-Domínguez, Raúl López-Domínguez, Iván Ellson. pathMED: Scoring Personalized Molecular Portraits. doi:10.18129/B9.bioc.pathMED, R package version 1.4.0, https://bioconductor.org/packages/pathMED.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pathMED")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.4.0 |
| License | GPL-2 |
| URL | https://github.com/jordimartorell/pathMED |
| Bug Reports | https://github.com/jordimartorell/pathMED/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 2399 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, FeatureExtraction, Pathways, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/pathMED/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pathMED")| A comprehensive framework for precision medicine with omics data | HTML | R Script |
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | pathMED_1.4.0.tar.gz |
| Windows binary (x86_64) | pathMED_1.4.0.zip |
| Source Repository | git clone https://git.bioconductor.org/packages/pathMED |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pathMED |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocParallel, caret, caretEnsemble, decoupleR, ggplot2, GSVA, factoextra, FactoMineR, magrittr, matrixStats, methods, metrica, pbapply, reshape2, singscore, stats, stringi, dplyr
Suggests: ada, AUCell, Biobase, BiocGenerics, BiocStyle, fgsea (>= 1.15.4), gam, GSEABase, import, kernlab, klaR, knitr, mboost, MLeval, randomForest, ranger, rmarkdown, RUnit, SummarizedExperiment, utils, xgboost