GenomicSuperSignature
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GenomicSuperSignature.
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Bioconductor version: 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>
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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics |
| Version | 1.0.1 |
| 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 |
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_1.0.1.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicSuperSignature/ |
| Package Short Url | https://bioconductor.org/packages/GenomicSuperSignature/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |