GenomicSuperSignature

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

Bioconductor version: Release (3.17)

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	1.8.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), SummarizedExperiment
Imports	ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba
Linking To
Suggests	knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils
System Requirements
Enhances
URL	https://github.com/shbrief/GenomicSuperSignature
Bug Reports	https://github.com/shbrief/GenomicSuperSignature/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GenomicSuperSignature_1.8.0.tar.gz
Windows Binary	GenomicSuperSignature_1.8.0.zip
macOS Binary (x86_64)	GenomicSuperSignature_1.8.0.tgz
macOS Binary (arm64)	GenomicSuperSignature_1.8.0.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