GenomicSuperSignature

DOI: 10.18129/B9.bioc.GenomicSuperSignature    

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

Bioconductor version: Release (3.13)

This package contains the index, which is the Replicable and interpretable Axes of Variation (RAV) extracted from public RNA sequencing datasets by clustering and averaging top PCs. This index, named as RAVindex, is further annotated with MeSH terms and GSEA. Functions to connect PCs from new datasets to RAVs, extract interpretable annotations, and provide intuitive visualization, are implemented in this package. Overall, this package enables researchers to analyze new data in the context of existing databases with minimal computing resources.

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 (!requireNamespace("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	1.0.1
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_1.0.1.tar.gz
Windows Binary	GenomicSuperSignature_1.0.1.zip
macOS 10.13 (High Sierra)	GenomicSuperSignature_1.0.1.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
Old Source Packages for BioC 3.13	Source Archive