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 (3.17)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel


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PDF R Script Using ssPATHS
PDF   Reference Manual


biocViews BiomedicalInformatics, Classification, DimensionReduction, GeneExpression, Pathways, RNASeq, Software, Transcriptomics
Version 1.13.0
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
Suggests ggplot2, testthat (>= 2.1.0)
Depends On Me
Imports Me
Suggests Me
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