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Bioconductor - GenomicSuperSignature (development version)

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 (3.22)

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 "4.5") and enter:


if (!require("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")
Details biocViews Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics Version 1.17.0 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License Artistic-2.0 Depends R (>= 4.1.0), SummarizedExperiment Imports ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba System Requirements URL https://github.com/shbrief/GenomicSuperSignature Bug Reports https://github.com/shbrief/GenomicSuperSignature/issues See More Suggests knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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