pathMED
Scoring Personalized Molecular Portraits
Bioconductor version: 3.23 · Package version: 1.4.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pathMED")Details
| Maintainer | Jordi Martorell-Marugán <jmartorellm@gmail.com> |
| Author | Jordi Martorell-Marugán [cre, aut] (ORCID: <https://orcid.org/0000-0002-5186-0735>), Daniel Toro-Domínguez [aut] (ORCID: <https://orcid.org/0000-0001-8440-312X>), Raúl López-Domínguez [aut] (ORCID: <https://orcid.org/0000-0001-8634-117X>), Iván Ellson [aut] (ORCID: <https://orcid.org/0000-0001-6307-3141>) |
| License | GPL-2 |
| URL | https://github.com/jordimartorell/pathMED |
| Bug Reports | https://github.com/jordimartorell/pathMED/issues |
| 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/ |
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.
Documentation
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 |
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