singscore

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Rank-based single-sample gene set scoring method

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-6398-9157 , Ruqian Lyu [aut, ctb], Momeneh Foroutan [aut, ctb] ORCID: 0000-0002-1440-0457 , Malvika Kharbanda [aut, cre] ORCID: 0000-0001-9726-3023

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

Citation (from within R, enter citation("singscore")):

Dharmesh D. Bhuva, Ruqian Lyu, Momeneh Foroutan, Malvika Kharbanda. singscore: Rank-based single-sample gene set scoring method. doi:10.18129/B9.bioc.singscore, R package version 1.32.0, https://bioconductor.org/packages/singscore.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Single sample scoring	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, Software
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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
System Requirements
URL	https://davislaboratory.github.io/singscore
Bug Reports	https://github.com/DavisLaboratory/singscore/issues

Suggests	pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
Linking To
Enhances
Depends On Me
Imports Me	GSABenchmark, pathMED, TBSignatureProfiler, xCell2
Suggests Me	clustermole, mastR, msigdb, vissE
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	singscore_1.32.0.tar.gz
Windows Binary (x86_64)	singscore_1.32.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	singscore_1.32.0.tgz
macOS Binary (sonoma-arm64)	singscore_1.32.0.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