ssPATHS

DOI: 10.18129/B9.bioc.ssPATHS    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ssPATHS.

ssPATHS: Single Sample PATHway Score

Bioconductor version: 3.15

This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set (pathway) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples.

Author: Natalie R. Davidson

Maintainer: Natalie R. Davidson <natalie.davidson at inf.ethz.ch>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ssPATHS")

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("ssPATHS")

 

PDF	R Script	Using ssPATHS
PDF		Reference Manual
Text		LICENSE

Details

biocViews	BiomedicalInformatics, Classification, DimensionReduction, GeneExpression, Pathways, RNASeq, Software, Transcriptomics
Version	1.10.0
In Bioconductor since	BioC 3.10 (R-3.6) (3 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), SummarizedExperiment
Imports	ROCR, dml, MESS
LinkingTo
Suggests	ggplot2, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ssPATHS_1.10.0.tar.gz
Windows Binary	ssPATHS_1.10.0.zip
macOS Binary (x86_64)	ssPATHS_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ssPATHS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ssPATHS
Package Short Url	https://bioconductor.org/packages/ssPATHS/
Package Downloads Report	Download Stats