GenomicSuperSignature
This is the released version of GenomicSuperSignature; for the devel version, see GenomicSuperSignature.
All Bioconductor versions of GenomicSuperSignature
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
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Bioconductor version: 3.23 · Package version: 1.20.0
This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.
Author: Sehyun Oh [aut, cre], Levi Waldron [aut], Sean Davis [aut]
Maintainer: Sehyun Oh <shbrief at gmail.com>
Citation
From within R, enter citation("GenomicSuperSignature"):
Sehyun Oh, Levi Waldron, Sean Davis. GenomicSuperSignature: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases. doi:10.18129/B9.bioc.GenomicSuperSignature, R package version 1.20.0, https://bioconductor.org/packages/GenomicSuperSignature.
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("GenomicSuperSignature")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.20.0 |
| License | Artistic-2.0 |
| URL | https://github.com/shbrief/GenomicSuperSignature |
| Bug Reports | https://github.com/shbrief/GenomicSuperSignature/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| Downloads rank | 891 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/GenomicSuperSignature/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomicSuperSignature")| Structure and content of RAVmodel | HTML | R Script |
| GenomicSuperSignature - Quickstart | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | GenomicSuperSignature_1.20.0.tar.gz |
| Windows binary (x86_64) | GenomicSuperSignature_1.20.0.zip |
| macOS binary (arm64) | GenomicSuperSignature_1.20.0.tgz |
| macOS binary (x86_64) | GenomicSuperSignature_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicSuperSignature |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicSuperSignature |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.1.0), SummarizedExperiment
Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba
Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils