GenomicSuperSignature
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Bioconductor version: Release (3.20)
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("GenomicSuperSignature")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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.
| Source Package | GenomicSuperSignature_1.14.0.tar.gz |
| Windows Binary (x86_64) | GenomicSuperSignature_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | GenomicSuperSignature_1.14.0.tgz |
| macOS Binary (arm64) | GenomicSuperSignature_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicSuperSignature |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicSuperSignature |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicSuperSignature/ |
| Package Short Url | https://bioconductor.org/packages/GenomicSuperSignature/ |
| Package Downloads Report | Download Stats |