{
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  "Package": "QuaternaryProd",
  "Type": "Package",
  "Title": "Computes the Quaternary Dot Product Scoring Statistic for Signed\nand Unsigned Causal Graphs",
  "Version": "1.47.0",
  "Date": "2015-10-22",
  "Authors@R": "c(\nperson(\"Carl Tony\", \"Fakhry\", email = \"cfakhry@cs.umb.edu\", role = c(\"cre\",\"aut\")),\nperson(\"Ping\", \"Chen\", role = \"ths\"),\nperson(\"Kourosh\", \"Zarringhalam\", role = c(\"aut\",\"ths\")))",
  "Description": "QuaternaryProd is an R package that performs causal\nreasoning on biological networks, including publicly available\nnetworks such as STRINGdb. QuaternaryProd is an open-source\nalternative to commercial products such as Inginuity Pathway\nAnalysis. For a given a set of differentially expressed genes,\nQuaternaryProd computes the significance of upstream regulators\nin the network by performing causal reasoning using the\nQuaternary Dot Product Scoring Statistic (Quaternary\nStatistic), Ternary Dot product Scoring Statistic (Ternary\nStatistic) and Fisher's exact test (Enrichment test). The\nQuaternary Statistic handles signed, unsigned and ambiguous\nedges in the network. Ambiguity arises when the direction of\ncausality is unknown, or when the source node (e.g., a protein)\nhas edges with conflicting signs for the same target gene. On\nthe other hand, the Ternary Statistic provides causal reasoning\nusing the signed and unambiguous edges only. The Vignette\nprovides more details on the Quaternary Statistic and\nillustrates an example of how to perform causal reasoning using\nSTRINGdb.",
  "License": "GPL (>=3)",
  "biocViews": "GraphAndNetwork, GeneExpression, Transcription",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "6.1.0",
  "Encoding": "UTF-8",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:24 UTC",
  "RemoteUrl": "https://github.com/bioc/QuaternaryProd",
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  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 07:01:59 UTC",
    "User": "root"
  },
  "Author": "Carl Tony Fakhry [cre, aut],\nPing Chen [ths],\nKourosh Zarringhalam [aut, ths]",
  "Maintainer": "Carl Tony Fakhry <cfakhry@cs.umb.edu>",
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    "geneexpression",
    "transcription",
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  ],
  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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  "_exports": [
    "QP_Pmf",
    "QP_Probability",
    "QP_Pvalue",
    "QP_SigPvalue",
    "QP_Support",
    "RunCRE_HSAStringDB"
  ],
  "_help": [
    {
      "page": "QuaternaryProd-package",
      "title": "Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs",
      "topics": [
        "QuaternaryProd-package"
      ]
    },
    {
      "page": "QP_Pmf",
      "title": "Computes the probability mass function of the scores.",
      "topics": [
        "QP_Pmf"
      ]
    },
    {
      "page": "QP_Probability",
      "title": "Computes the probability of a score.",
      "topics": [
        "QP_Probability"
      ]
    },
    {
      "page": "QP_Pvalue",
      "title": "Computes the p-value of a score.",
      "topics": [
        "QP_Pvalue"
      ]
    },
    {
      "page": "QP_SigPvalue",
      "title": "Computes the p-value for a statistically significant score.",
      "topics": [
        "QP_SigPvalue"
      ]
    },
    {
      "page": "QP_Support",
      "title": "Computes the support for the scores.",
      "topics": [
        "QP_Support"
      ]
    },
    {
      "page": "RunCRE_HSAStringDB",
      "title": "This function runs a causal relation engine by computing the Quaternary Dot Product Scoring Statistic, Ternary Dot Product Scoring Statistic or the Enrichment test over the Homo Sapien STRINGdb causal network (version 10 provided under the Creative Commons license: https://creativecommons.org/licenses/by/3.0/). Note that the user has the option of specifying other causal networks with this function.",
      "topics": [
        "RunCRE_HSAStringDB"
      ]
    }
  ],
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    "dplyr",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
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    "Rcpp",
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    "vctrs",
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      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
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    {
      "source": "QuaternaryProdVignette.Rmd",
      "filename": "QuaternaryProdVignette.pdf",
      "title": "QuaternaryProd",
      "author": "Carl Tony Fakhry, Ping Chen and Kourosh Zarringhalam",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Functionality",
        "Functionality for working with the Homo sapien causal network from STRINGdb",
        "Compute Pvalues Over the Network",
        "Load Gene Expression Data",
        "Compute the Quaternary Dot Product Scoring Statistic over STRINGdb",
        "Compute the Ternary Dot Product Scoring Statistic and the Enrichment test over STRINGdb",
        "References"
      ],
      "created": "2015-10-29 22:19:18",
      "modified": "2018-09-14 04:15:22",
      "commits": 17
    }
  ],
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  "_indexed": true,
  "_nocasepkg": "quaternaryprod",
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