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singscore

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

Rank-based single-sample gene set scoring method


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneExpression, GeneSetEnrichment, Software
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
See More
Suggests pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
Linking To
Enhances
Depends On Me
Imports Me SingscoreAMLMutations, TBSignatureProfiler
Suggests Me mastR, msigdb, vissE
Links To Me
Build Report Build Report

Package Archives

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

Source Package singscore_1.23.0.tar.gz
Windows Binary singscore_1.23.0.zip
macOS Binary (x86_64) singscore_1.23.0.tgz
macOS Binary (arm64) singscore_1.23.0.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