pathMED
This is the development version of pathMED; to use it, please install the devel version of Bioconductor.
Scoring Personalized Molecular Portraits
Bioconductor version: Development (3.21)
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("pathMED")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("pathMED")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pathMED")| pathMED | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, FeatureExtraction, Pathways, Software, Transcriptomics |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | GPL-2 |
| Depends | R (>= 4.5.0) |
| Imports | BiocParallel, caret, caretEnsemble, decoupleR, ggplot2, GSVA, factoextra, FactoMineR, magrittr, matrixStats, methods, metrica, pbapply, reshape2, singscore, stats, stringi, dplyr |
| System Requirements | |
| URL | https://github.com/jordimartorell/pathMED |
| Bug Reports | https://github.com/jordimartorell/pathMED/issues |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pathMED_0.99.2.tar.gz |
| Windows Binary (x86_64) | pathMED_0.99.2.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/pathMED |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pathMED |
| Bioc Package Browser | https://code.bioconductor.org/browse/pathMED/ |
| Package Short Url | https://bioconductor.org/packages/pathMED/ |
| Package Downloads Report | Download Stats |