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Bioconductor - sSNAPPY (development version)

sSNAPPY

This is the development version of sSNAPPY; for the stable release version, see sSNAPPY.

Single Sample directioNAl Pathway Perturbation analYsis

Bioconductor version: Development (3.22)

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 (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")

# 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 PDF NEWS Text Details biocViews GeneExpression, GeneSetEnrichment, GeneSignaling, Software Version 1.13.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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.

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