singscore
Rank-based single-sample gene set scoring method
Bioconductor version: Release (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("singscore")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 |
See More
| Suggests | pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | TBSignatureProfiler, 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.
| Source Package | singscore_1.24.0.tar.gz |
| Windows Binary (x86_64) | singscore_1.24.0.zip |
| macOS Binary (x86_64) | singscore_1.24.0.tgz |
| macOS Binary (arm64) | singscore_1.24.0.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 |