sSNAPPY

DOI: 10.18129/B9.bioc.sSNAPPY  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see sSNAPPY.

Single Sample directioNAl Pathway Perturbation analYsis

Bioconductor version: 3.16

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 directions of changes.Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.

Author: Wenjun Liu [aut, cre]

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

Installation

To install this package, start R (version "4.2") 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	1.2.5
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	dplyr, magrittr, rlang, stats, purrr, BiocParallel, graphite, Rcpp, tibble, ggplot2, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, ggnewscale, pheatmap, utils
LinkingTo	Rcpp, RcppArmadillo
Suggests	BiocManager, BiocStyle, cowplot, DT, htmltools, knitr, pander, rmarkdown, spelling, stringr, 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_1.2.5.tar.gz
Windows Binary	sSNAPPY_1.2.5.zip
macOS Binary (x86_64)	sSNAPPY_1.2.5.tgz
macOS Binary (arm64)	sSNAPPY_1.2.5.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