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GenomicSuperSignature

Interpretation of RNA-seq experiments through robust, efficient comparison to public databases


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicSuperSignature")
Introduction on RAVmodel HTML R Script
Quickstart HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0
Depends R (>= 4.1.0), SummarizedExperiment
Imports ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba
System Requirements
URL https://github.com/shbrief/GenomicSuperSignature
Bug Reports https://github.com/shbrief/GenomicSuperSignature/issues
See More
Suggests knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils
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Package Archives

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

Source Package GenomicSuperSignature_1.10.0.tar.gz
Windows Binary GenomicSuperSignature_1.10.0.zip
macOS Binary (x86_64) GenomicSuperSignature_1.10.0.tgz
macOS Binary (arm64) GenomicSuperSignature_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicSuperSignature
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicSuperSignature
Bioc Package Browser https://code.bioconductor.org/browse/GenomicSuperSignature/
Package Short Url https://bioconductor.org/packages/GenomicSuperSignature/
Package Downloads Report Download Stats