sSNAPPY
This is the development version of sSNAPPY; for the stable release version, see sSNAPPY.
Single Sample directioNAl Pathway Perturbation analYsis
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.17.0 |
| 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 |
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_1.17.0.tar.gz |
| Windows Binary (x86_64) | sSNAPPY_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | sSNAPPY_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | sSNAPPY_1.17.0.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 |