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Single Sample directioNAl Pathway Perturbation analYsis

Bioconductor version: Release (3.19)

A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.

Author: Wenjun Liu [aut, cre] , Stephen Pederson [aut]

Maintainer: Wenjun Liu <wenjun.liu at>

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Reference Manual PDF


biocViews GeneExpression, GeneSetEnrichment, GeneSignaling, Software
Version 1.8.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.3.0), ggplot2
Imports dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble, ggraph, igraph, reshape2,, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr
System Requirements C++11
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Suggests BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse
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