Registration Open for Bioc2024 July 24-26


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

ssPATHS: Single Sample PATHway Score

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Using ssPATHS PDF R Script
Reference Manual PDF


biocViews BiomedicalInformatics, Classification, DimensionReduction, GeneExpression, Pathways, RNASeq, Software, Transcriptomics
Version 1.19.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), SummarizedExperiment
Imports ROCR, dml, MESS
System Requirements
See More
Suggests ggplot2, testthat (>= 2.1.0)
Linking To
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 ssPATHS_1.19.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ssPATHS_1.19.0.tgz
macOS Binary (arm64) ssPATHS_1.19.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats