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Single Sample directioNAl Pathway Perturbation analYsis

Bioconductor version: Release (3.18)

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 adelaide.edu.au>

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


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


biocViews GeneExpression, GeneSetEnrichment, GeneSignaling, Software
Version 1.6.1
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, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr
System Requirements C++11
URL https://wenjun-liu.github.io/sSNAPPY/
Bug Reports https://github.com/Wenjun-Liu/sSNAPPY/issues
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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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Follow Installation instructions to use this package in your R session.

Source Package sSNAPPY_1.6.1.tar.gz
Windows Binary sSNAPPY_1.6.1.zip
macOS Binary (x86_64) sSNAPPY_1.6.1.tgz
macOS Binary (arm64) sSNAPPY_1.6.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/sSNAPPY
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sSNAPPY
Bioc Package Browser https://code.bioconductor.org/browse/sSNAPPY/
Package Short Url https://bioconductor.org/packages/sSNAPPY/
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Old Source Packages for BioC 3.18 Source Archive