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

DOI: 10.18129/B9.bioc.GenomicSuperSignature

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>

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

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")

Introduction on RAVmodel HTML R Script

Quickstart HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics

Version 1.2.1

In Bioconductor since BioC 3.13 (R-4.1) (3 years)

License Artistic-2.0

Depends R (>= 4.0), SummarizedExperiment

Imports ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable

System Requirements

URL https://github.com/shbrief/GenomicSuperSignature

Bug Reports https://github.com/shbrief/GenomicSuperSignature/issues

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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