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  "Package": "signatureSearch",
  "Title": "Environment for Gene Expression Searching Combined with\nFunctional Enrichment Analysis",
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  "Authors@R": "c(person(\"Yuzhu\", \"Duan\", email = \"yduan004@ucr.edu\",\nrole = c(\"aut\")),\nperson(\"Brendan\", \"Gongol\", email = \"bgong001@ucr.edu\",\nrole = c(\"cre\", \"aut\")),\nperson(\"Thomas\", \"Girke\", email = \"thomas.girke@ucr.edu\",\nrole = \"aut\"))",
  "Description": "This package implements algorithms and data structures for\nperforming gene expression signature (GES) searches, and\nsubsequently interpreting the results functionally with\nspecialized enrichment methods.",
  "License": "Artistic-2.0",
  "SystemRequirements": "C++20",
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  "URL": "https://github.com/yduan004/signatureSearch/",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:25 UTC",
  "RemoteUrl": "https://github.com/bioc/signatureSearch",
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  "Author": "Yuzhu Duan [aut],\nBrendan Gongol [cre, aut],\nThomas Girke [aut]",
  "Maintainer": "Brendan Gongol <bgong001@ucr.edu>",
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    "gseReactome",
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    "meanExpr2h5",
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    "parse_gctx",
    "qSig",
    "rand_query_ES",
    "read_gmt",
    "result",
    "runWF",
    "set_readable",
    "show",
    "sim_score_grp",
    "tarReduce",
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    "tsea_mabs",
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      "page": "signatureSearch-package",
      "title": "Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis",
      "topics": [
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        "signatureSearch"
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    },
    {
      "page": "sub-.feaResult",
      "title": "Subset a feaResult object by index",
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        "[.feaResult"
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    {
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      "topics": [
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        "$.feaResult"
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      "page": "add_pcid",
      "title": "Add PCID to drug data frame",
      "topics": [
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      "title": "Add Compound Annotation Info to GESS Result Table",
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    {
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      "title": "Add MOA annotation to drug data frame",
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    },
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      "page": "dim-methods",
      "title": "Dimensions of an Object",
      "topics": [
        "dim",
        "dim,feaResult-method",
        "dim,gessResult-method"
      ]
    },
    {
      "page": "drug_cell_ranks",
      "title": "Summary ranking statistics across cell types",
      "topics": [
        "drug_cell_ranks"
      ]
    },
    {
      "page": "drugs-methods",
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        "drugs,feaResult,ANY-method",
        "drugs,feaResult-method",
        "drugs<-",
        "drugs<-,feaResult-method"
      ]
    },
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        "drugs10"
      ]
    },
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        "dsea_hyperG",
        "tsea_dup_hyperG",
        "tsea_mabs",
        "tsea_mGSEA"
      ]
    },
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      "page": "dtnetplot",
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        "dtnetplot"
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      "page": "enrichGO2",
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        "enrichGO2"
      ]
    },
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      "page": "enrichMOA",
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      ]
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        "enrichReactome"
      ]
    },
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      "page": "get_targets",
      "title": "Target Gene/Protein IDs for Query Drugs",
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      "title": "Class \"qSig\"",
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    },
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      "topics": [
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      "page": "read_gmt",
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      "title": "Method to Extract Result Slots",
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      "page": "runWF",
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    {
      "page": "set_readable",
      "title": "Set Readable",
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    },
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      "page": "show-methods",
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      "page": "targetList",
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      ]
    },
    {
      "page": "tarReduce",
      "title": "Show Reduced Targets",
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    },
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      "page": "vec_char_redu",
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    {
      "source": "signatureSearch.Rmd",
      "filename": "signatureSearch.html",
      "title": "signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis",
      "author": "Authors: Yuzhu Duan, Brendan Gongol, Dan S. Evans, Richard A. Miller, Nicholas J. Schork, Steven R. Cummings and Thomas Girke",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Background",
        "Motivation and Design",
        "History of GES Databases",
        "Terminology",
        "Getting Started",
        "Package Install",
        "Reference Databases",
        "Signature Searches (GESS)",
        "Test Query and Database",
        "CMAP Search Method",
        "LINCS Search Method",
        "gCMAP Search Method",
        "Fisher Search Method",
        "Correlation-based Search Method",
        "CORall",
        "CORsub",
        "Summary of Search Results",
        "GESS Result Visualization",
        "Batch Processing of GESSs",
        "Sequential Processing",
        "Parallelization with Multiple CPU Cores",
        "Parallelization with Multiple Computer Systems",
        "Functional Enrichment (FEA)",
        "TSEA",
        "Hypergeometric Test",
        "With GO",
        "With Reactome",
        "mGSEA Method",
        "MeanAbs Method",
        "DSEA",
        "GSEA Method",
        "Comparing FEA Results",
        "Summary of FEA Results",
        "Drug-Target Network Visualization",
        "Run Workflow",
        "Additional Databases",
        "Gene Set Databases",
        "Overview",
        "Gene Sets as Queries",
        "Gene Sets as Database",
        "MSigDB",
        "GSKB",
        "Supplemental Material",
        "Construction of Toy Database",
        "Session Info",
        "Funding",
        "References"
      ],
      "created": "2018-10-05 23:19:37",
      "modified": "2026-01-29 20:42:11",
      "commits": 104
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