sSNAPPY

This is the released version of sSNAPPY; for the devel version, see sSNAPPY.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

Single Sample directioNAl Pathway Perturbation analYsis

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-8185-3069 , Stephen Pederson [aut] ORCID: 0000-0001-8197-3303

Maintainer: Wenjun Liu <wenjun.liu at adelaide.edu.au>

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

Wenjun Liu, Stephen Pederson. sSNAPPY: Single Sample directioNAl Pathway Perturbation analYsis. doi:10.18129/B9.bioc.sSNAPPY, R package version 1.16.0, https://bioconductor.org/packages/sSNAPPY.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, GeneSignaling, Software
Version	1.16.0
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 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
System Requirements	C++11
URL	https://wenjun-liu.github.io/sSNAPPY/
Bug Reports	https://github.com/Wenjun-Liu/sSNAPPY/issues

Suggests	BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	sSNAPPY_1.16.0.tar.gz
Windows Binary (x86_64)	sSNAPPY_1.16.0.zip
macOS Binary (big-sur-x86_64)	sSNAPPY_1.16.0.tgz
macOS Binary (sonoma-arm64)	sSNAPPY_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sSNAPPY
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sSNAPPY
Package Short Url	https://bioconductor.org/packages/sSNAPPY/
Package Downloads Report	Download Stats