GenomicSuperSignature

DOI: 10.18129/B9.bioc.GenomicSuperSignature    

This is the development version of GenomicSuperSignature; for the stable release version, see GenomicSuperSignature.

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

Bioconductor version: Development (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>

Citation (from within R, enter citation("GenomicSuperSignature")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.8
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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_1.1.8.tar.gz
Windows Binary GenomicSuperSignature_1.1.8.zip
macOS 10.13 (High Sierra) GenomicSuperSignature_1.1.7.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

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