sSNAPPY
This is thereleased version of sSNAPPY; for the devel version, seesSNAPPY.
Single Sample directioNAl Pathway Perturbation analYsis
Bioconductor version: Release (3.22)
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("sSNAPPY")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("sSNAPPY")For older versions of R, please refer to the appropriateBioconductor 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 | 1.14.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (3.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | sSNAPPY_1.14.0.tar.gz |
| Windows Binary (x86_64) | sSNAPPY_1.14.0.zip |
| macOS Binary (x86_64) | sSNAPPY_1.14.0.tgz |
| macOS Binary (arm64) | sSNAPPY_1.14.0.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 |