singscore

DOI: 10.18129/B9.bioc.singscore    

Rank-based single-sample gene set scoring method

Bioconductor version: Release (3.13)

A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample's gene expression profile. It scores the expression activities of gene sets at a single-sample level.

Author: Ruqian Lyu [aut, ctb], Momeneh Foroutan [aut, ctb] , Dharmesh D. Bhuva [aut, cre]

Maintainer: Dharmesh D. Bhuva <bhuva.d at wehi.edu.au>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("singscore")

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("singscore")

 

HTML	R Script	Single sample scoring
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneSetEnrichment, Software
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://davislaboratory.github.io/singscore
BugReports	https://github.com/DavisLaboratory/singscore/issues
Depends On Me
Imports Me	SingscoreAMLMutations, TBSignatureProfiler
Suggests Me	msigdb, vissE
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	singscore_1.12.0.tar.gz
Windows Binary	singscore_1.12.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	singscore_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/singscore
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/singscore
Package Short Url	https://bioconductor.org/packages/singscore/
Package Downloads Report	Download Stats