{
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  "Package": "GenomicSuperSignature",
  "Title": "Interpretation of RNA-seq experiments through robust, efficient\ncomparison to public databases",
  "Authors@R": "c(\nperson(\"Sehyun\", \"Oh\", email = \"shbrief@gmail.com\", role = c(\"aut\",\"cre\")),\nperson(\"Levi\", \"Waldron\", role = \"aut\"),\nperson(\"Sean\", \"Davis\", email = \"seandavi@gmail.com\", role = \"aut\"))",
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  "Date": "2025-9-30",
  "Description": "This package provides a novel method for interpreting new\ntranscriptomic datasets through near-instantaneous comparison\nto public archives without high-performance computing\nrequirements. Through the pre-computed index, users can\nidentify public resources associated with their dataset such as\ngene sets, MeSH term, and publication. Functions to identify\ninterpretable annotations and intuitive visualization options\nare implemented in this package.",
  "License": "Artistic-2.0",
  "biocViews": "Transcriptomics, SystemsBiology, PrincipalComponent, RNASeq,\nSequencing, Pathways, Clustering",
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  "URL": "https://github.com/shbrief/GenomicSuperSignature",
  "BugReports": "https://github.com/shbrief/GenomicSuperSignature/issues",
  "Collate": "'GenomicSignatures-class.R' 'GenomicSignatures-methods.R'\n'PCAGenomicSignatures-methods.R' 'annotatePC.R' 'annotateRAV.R'\n'availableRAVmodel.R' 'buildAvgLoading.R' 'calculateScore.R'\n'data.R' 'drawWordcloud.R' 'extractPC.R' 'findSignature.R'\n'findStudiesInCluster.R' 'getMetadata.R' 'getModel.R'\n'heatmapTable.R' 'plotAnnotatedPCA.R' 'plotValidate.R'\n'rmNaInf.R' 'sampleScoreHeatmap.R' 'subsetEnrichedPathways.R'\n'utils.R' 'validate.R' 'validatedSignatures.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:16 UTC",
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    "subsetEnrichedPathways",
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    "validate",
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      "title": "List the available RAVmodels",
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      "title": "Calculate average loadings of each cluster",
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      "title": "Calculate the validation score for a new dataset",
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      "title": "Draw wordcloud using the collection of RAVs' MeSH terms",
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      "page": "droplist",
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      "page": "extractPC",
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      "page": "filterList",
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    {
      "page": "getRAVInfo",
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      "page": "getStudyInfo",
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      "page": "heatmapTable",
      "title": "Validation result in heatmap format",
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      "page": "meshTable",
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      "page": "miniAllZ",
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      "page": "miniRAVmodel",
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      "page": "miniTCGA",
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      "page": "PCAGenomicSignatures",
      "title": "Construct 'PCAGenomicSignatures' object",
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      "page": "PCinRAV",
      "title": "Extract the list of PCs in a cluster",
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    {
      "page": "plotAnnotatedPCA",
      "title": "Two-dimensional PCA plot with the PC annotation",
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      "page": "plotValidate",
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      "source": "Contents.Rmd",
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      "title": "Structure and content of RAVmodel",
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      "headings": [
        "Citing GenomicSuperSignature",
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        "Download RAVmodel",
        "Content of RAVmodel",
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        "Metadata for RAVmodel",
        "Studies in each RAV",
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      "headings": [
        "Setup",
        "Install and load package",
        "Download RAVmodel",
        "Example dataset",
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        "Interactive Graph",
        "What kinds of information can you access through RAV?",
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      "modified": "2022-07-26 23:21:53",
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