GenomicSuperSignature

DOI: 10.18129/B9.bioc.GenomicSuperSignature    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see GenomicSuperSignature.

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

Bioconductor version: 3.14

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	Introduction on RAVmodel
HTML	R Script	Quickstart
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics
Version	1.2.1
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	Artistic-2.0
Depends	R (>= 4.0), SummarizedExperiment
Imports	ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable
LinkingTo
Suggests	knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils
SystemRequirements
Enhances
URL	https://github.com/shbrief/GenomicSuperSignature
BugReports	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_1.2.1.tar.gz
Windows Binary	GenomicSuperSignature_1.2.1.zip
macOS 10.13 (High Sierra)	GenomicSuperSignature_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicSuperSignature
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomicSuperSignature
Package Short Url	https://bioconductor.org/packages/GenomicSuperSignature/
Package Downloads Report	Download Stats