sSNAPPY
Single Sample directioNAl Pathway Perturbation analYsis
Bioconductor version: Release (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("sSNAPPY")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | GeneExpression, GeneSetEnrichment, GeneSignaling, Software |
Version | 1.8.0 |
In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
See More
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 |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | sSNAPPY_1.8.0.tar.gz |
Windows Binary | sSNAPPY_1.8.0.zip |
macOS Binary (x86_64) | sSNAPPY_1.8.0.tgz |
macOS Binary (arm64) | sSNAPPY_1.8.0.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 3.19 | Source Archive |