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: 1.0.1
Date: 2021-05-27
Description: 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.
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
License: Artistic-2.0
biocViews: Transcriptomics, SystemsBiology, PrincipalComponent, RNASeq,
        Sequencing, Pathways, Clustering
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1.9000
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'
        'annotatePCcluster.R' 'buildAvgLoading.R' 'calculateScore.R'
        'data.R' 'drawWordcloud.R' 'extractPC.R' 'findSignature.R'
        'findStudiesInCluster.R' 'funcForGSEA.R' 'getModel.R'
        'heatmapTable.R' 'plotAnnotedPCA.R' 'plotValidate.R'
        'rmNaInf.R' 'rowNorm.R' 'sampleScoreHeatmap.R'
        'subsetEnrichedPathways.R' 'utils.R' 'validate.R'
        'validatedSignatures.R'
git_url: https://git.bioconductor.org/packages/GenomicSuperSignature
git_branch: RELEASE_3_13
git_last_commit: 56891d8
git_last_commit_date: 2021-05-27
Date/Publication: 2021-05-27
NeedsCompilation: no
Packaged: 2021-05-27 20:00:23 UTC; biocbuild
Author: Sehyun Oh [aut, cre],
  Levi Waldron [aut],
  Sean Davis [aut]
Maintainer: Sehyun Oh <shbrief@gmail.com>
Built: R 4.1.0; ; 2021-05-28 10:08:07 UTC; unix
