Registration Open for Bioc2024
Early registration discount pricing ends May 31!


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

Single Sample directioNAl Pathway Perturbation analYsis

Bioconductor version: Development (3.20)

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>

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


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:

Single Sample Directional Pathway Perturbation Analysis HTML R Script
Reference Manual PDF


biocViews GeneExpression, GeneSetEnrichment, GeneSignaling, Software
Version 1.9.0
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
Bug Reports
See More
Suggests BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse
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 sSNAPPY_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64) sSNAPPY_1.9.0.tgz
macOS Binary (arm64) sSNAPPY_1.9.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats