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Bioconductor - singscore

singscore

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

Rank-based single-sample gene set scoring method

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews GeneExpression, GeneSetEnrichment, Software Version 1.28.0 In Bioconductor since BioC 3.7 (R-3.5) (7 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 pathMED, TBSignatureProfiler, xCell2, SingscoreAMLMutations, clustermole, GSEMA Suggests Me mastR, vissE, msigdb Links To Me Build Report Build Report Package Archives

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

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