sSNAPPY

This is the released version of sSNAPPY; for the devel version, see sSNAPPY.

Single Sample directioNAl Pathway Perturbation analYsis

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DOI: 10.18129/B9.bioc.sSNAPPY

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 iD ORCID: 0000-0002-8185-3069 , Stephen Pederson [aut] ORCID iD ORCID: 0000-0001-8197-3303

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

Citation (from within R, enter 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 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

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

Suggests BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse

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Package Archives

Follow Installation 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 (64-bit only)

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/

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