sSNAPPY

DOI: 10.18129/B9.bioc.sSNAPPY  

Single Sample directioNAl Pathway Perturbation analYsis

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	GeneExpression, GeneSetEnrichment, GeneSignaling, Software
Version	1.4.6
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 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
LinkingTo
Suggests	BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse
SystemRequirements	C++11
Enhances
URL	https://wenjun-liu.github.io/sSNAPPY/
BugReports	https://github.com/Wenjun-Liu/sSNAPPY/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	sSNAPPY_1.4.6.tar.gz
Windows Binary	sSNAPPY_1.4.6.zip
macOS Binary (x86_64)	sSNAPPY_1.4.6.tgz
macOS Binary (arm64)	sSNAPPY_1.4.6.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
Old Source Packages for BioC 3.17	Source Archive