sSNAPPY
This is the development version of sSNAPPY; for the stable release version, see sSNAPPY.
Single Sample directioNAl Pathway Perturbation analYsis
Bioconductor version: Development (3.21)
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:
Maintainer: Wenjun Liu <wenjun.liu at adelaide.edu.au>
citation("sSNAPPY")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, GeneSignaling, Software |
| Version | 1.11.0 |
| 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |