singscore

DOI: 10.18129/B9.bioc.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 (3.14)

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>

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

Installation

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

if (!requireNamespace("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")

 

HTML R Script Single sample scoring
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, GeneSetEnrichment, Software
Version 1.13.1
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 hexbin, 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_1.13.1.tar.gz
Windows Binary singscore_1.13.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) singscore_1.13.1.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

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