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sSNAPPY

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

Single Sample directioNAl Pathway Perturbation analYsis


Bioconductor version: Development (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 adelaide.edu.au>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("sSNAPPY")

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

Documentation

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

browseVignettes("sSNAPPY")
Single Sample Directional Pathway Perturbation Analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneSetEnrichment, GeneSignaling, Software
Version 1.7.1
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
See More
Suggests BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package sSNAPPY_1.7.1.tar.gz
Windows Binary sSNAPPY_1.7.1.zip
macOS Binary (x86_64) sSNAPPY_1.7.1.tgz
macOS Binary (arm64) sSNAPPY_1.7.1.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/
Package Downloads Report Download Stats