singscore

DOI: 10.18129/B9.bioc.singscore  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see singscore.

Rank-based single-sample gene set scoring method

Bioconductor version: 3.17

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

Maintainer: Malvika Kharbanda <kharbanda.m at wehi.edu.au>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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	1.20.0
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 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	pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
SystemRequirements
Enhances
URL	https://davislaboratory.github.io/singscore
BugReports	https://github.com/DavisLaboratory/singscore/issues
Depends On Me
Imports Me	SingscoreAMLMutations, TBSignatureProfiler
Suggests Me	mastR, msigdb, vissE
Links To Me
Build Report

Package Archives

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

Source Package	singscore_1.20.0.tar.gz
Windows Binary	singscore_1.20.0.zip
macOS Binary (x86_64)	singscore_1.20.0.tgz
macOS Binary (arm64)	singscore_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/singscore
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/singscore
Bioc Package Browser	https://code.bioconductor.org/browse/singscore/
Package Short Url	https://bioconductor.org/packages/singscore/
Package Downloads Report	Download Stats