ssPATHS

DOI: 10.18129/B9.bioc.ssPATHS    

This is the development version of ssPATHS; for the stable release version, see ssPATHS.

ssPATHS: Single Sample PATHway Score

Bioconductor version: Development (3.11)

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>

Citation (from within R, enter citation("ssPATHS")):

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends 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_1.1.0.tar.gz
Windows Binary ssPATHS_1.1.0.zip
Mac OS X 10.11 (El Capitan) ssPATHS_1.1.0.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

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