This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GenomicSuperSignature.
Bioconductor version: 3.17
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")
):
To install this package, start R (version "4.3") 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.
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 |
Reference Manual | ||
Text | NEWS |
biocViews | Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics |
Version | 1.8.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (2.5 years) |
License | Artistic-2.0 |
Depends | R (>= 4.1.0), SummarizedExperiment |
Imports | ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | GenomicSuperSignature_1.8.0.tar.gz |
Windows Binary | GenomicSuperSignature_1.8.0.zip |
macOS Binary (x86_64) | GenomicSuperSignature_1.8.0.tgz |
macOS Binary (arm64) | GenomicSuperSignature_1.8.0.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 |
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