Package: GenomicSuperSignature
Title: Interpretation of RNA-seq experiments through robust, efficient
        comparison to public databases
Authors@R: c(
  person("Sehyun", "Oh", email = "shbrief@gmail.com", role = c("aut","cre")),
  person("Levi", "Waldron", role = "aut"),
  person("Sean", "Davis", email = "seandavi@gmail.com", role = "aut"))
Version: 1.18.0
Date: 2025-9-30
Description: 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.
Depends: R (>= 4.1.0), SummarizedExperiment
Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr,
        dplyr, plotly, BiocFileCache, grid, flextable, irlba
Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis,
        BiocStyle, testthat, forcats, stats, wordcloud, circlize,
        EnrichmentBrowser, clusterProfiler, msigdbr, cluster,
        RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr,
        utils
License: Artistic-2.0
biocViews: Transcriptomics, SystemsBiology, PrincipalComponent, RNASeq,
        Sequencing, Pathways, Clustering
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/shbrief/GenomicSuperSignature
BugReports: https://github.com/shbrief/GenomicSuperSignature/issues
Collate: 'GenomicSignatures-class.R' 'GenomicSignatures-methods.R'
        'PCAGenomicSignatures-methods.R' 'annotatePC.R' 'annotateRAV.R'
        'availableRAVmodel.R' 'buildAvgLoading.R' 'calculateScore.R'
        'data.R' 'drawWordcloud.R' 'extractPC.R' 'findSignature.R'
        'findStudiesInCluster.R' 'getMetadata.R' 'getModel.R'
        'heatmapTable.R' 'plotAnnotatedPCA.R' 'plotValidate.R'
        'rmNaInf.R' 'sampleScoreHeatmap.R' 'subsetEnrichedPathways.R'
        'utils.R' 'validate.R' 'validatedSignatures.R'
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev make libharfbuzz-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libwebp-dev libxml2-dev
        libssl-dev perl zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:09:57 UTC
RemoteUrl: https://github.com/bioc/GenomicSuperSignature
RemoteRef: RELEASE_3_22
RemoteSha: e2b134e3dee77e86f65d27b13bc0d7e5980f77a4
NeedsCompilation: no
Packaged: 2026-02-24 08:30:38 UTC; root
Author: Sehyun Oh [aut, cre],
  Levi Waldron [aut],
  Sean Davis [aut]
Maintainer: Sehyun Oh <shbrief@gmail.com>
Built: R 4.5.2; ; 2026-02-24 08:33:35 UTC; windows
