Bioconductor - pathMED

Bioconductor - pathMED
Bioconductor 3.22
Software Packages
pathMED
pathMED
This is the
released
version of pathMED; for the devel version, see
pathMED
Scoring Personalized Molecular Portraits
DOI:
10.18129/B9.bioc.pathMED
Bioconductor version:
Release (3.22)
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]
ORCID: 0000-0002-5186-0735
, Daniel Toro-Domínguez [aut]
ORCID: 0000-0001-8440-312X
, Raúl López-Domínguez [aut]
ORCID: 0000-0001-8634-117X
, Iván Ellson [aut]
ORCID: 0000-0001-6307-3141
Maintainer:
Jordi Martorell-Marugán
Citation (from within R, enter
citation("pathMED")
):
Installation
To install this package, start R (version "4.5") 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
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
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
Classification
FeatureExtraction
Pathways
Software
Transcriptomics
Version
1.2.0
In Bioconductor since
BioC 3.21 (R-4.5) (1 year)
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
Bug Reports
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_1.2.0.tar.gz
Windows Binary (x86_64)
pathMED_1.2.0.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
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