DOI: 10.18129/B9.bioc.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>

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


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HTML R Script Introduction on RAVmodel
HTML R Script Quickstart
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biocViews Clustering, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, SystemsBiology, Transcriptomics
Version 1.0.1
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License Artistic-2.0
Depends R (>= 4.0), SummarizedExperiment
Imports ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable
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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