{
  "_id": "6a196941acfb0bcc41de8f4b",
  "Package": "CeTF",
  "Type": "Package",
  "Title": "Coexpression for Transcription Factors using Regulatory Impact\nFactors and Partial Correlation and Information Theory analysis",
  "Version": "1.25.0",
  "Authors@R": "c(person(\"Carlos Alberto\", \"Oliveira de Biagi Junior\", email = \n\"cbiagijr@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Ricardo\", \"Perecin\nNociti\", email = \"rnociti@gmail.com\", role = c(\"aut\")), person(\"Breno\",\n\"Osvaldo Funicheli\", email = \"osvaldobreno99@gmail.com \", role = c(\"aut\")),\nperson(\"João Paulo\", \"Bianchi Ximenez\", email = \"joaopaulo.ximenez@me.com\",\nrole = c(\"ctb\")), person(\"Patrícia\", \"de Cássia Ruy\", email =\n\"patiruy@gmail.com\", role = c(\"ctb\")), person(\"Marcelo\", \"Gomes de Paula\",\nemail = \"marcelogomesrp@gmail.com\", role = c(\"ctb\")), person(\"Rafael\", \"dos\nSantos Bezerra\", email = \"rafaelbezerra50@yahoo.com\", role = c(\"ctb\")),\nperson(\"Wilson\", \"Araújo da Silva Junior\", email = \"wilsonjr@usp.br\", role =\nc(\"aut\", \"ths\")))",
  "Description": "This package provides the necessary functions for\nperforming the Partial Correlation coefficient with Information\nTheory (PCIT) (Reverter and Chan 2008) and Regulatory Impact\nFactors (RIF) (Reverter et al. 2010) algorithm. The PCIT\nalgorithm identifies meaningful correlations to define edges in\na weighted network and can be applied to any correlation-based\nnetwork including but not limited to gene co-expression\nnetworks, while the RIF algorithm identify critical\nTranscription Factors (TF) from gene expression data. These two\nalgorithms when combined provide a very relevant layer of\ninformation for gene expression studies (Microarray, RNA-seq\nand single-cell RNA-seq data).",
  "SystemRequirements": "libcurl4-openssl-dev, libxml2-dev, libssl-dev,\ngfortran, build-essential, libz-dev, zlib1g-dev",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.2.3",
  "biocViews": "Sequencing, RNASeq, Microarray, GeneExpression,\nTranscription, Normalization, DifferentialExpression,\nSingleCell, Network, Regression, ChIPSeq, ImmunoOncology,\nCoverage",
  "VignetteBuilder": "knitr",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:33 UTC",
  "RemoteUrl": "https://github.com/bioc/CeTF",
  "RemoteRef": "HEAD",
  "RemoteSha": "13787a4c8c56a671ef45a5ba4321de67b6576f60",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 08:33:14 UTC",
    "User": "root"
  },
  "Author": "Carlos Alberto Oliveira de Biagi Junior [aut, cre],\nRicardo Perecin Nociti [aut],\nBreno Osvaldo Funicheli [aut],\nJoão Paulo Bianchi Ximenez [ctb],\nPatrícia de Cássia Ruy [ctb],\nMarcelo Gomes de Paula [ctb],\nRafael dos Santos Bezerra [ctb],\nWilson Araújo da Silva Junior [aut, ths]",
  "Maintainer": "Carlos Alberto Oliveira de Biagi Junior <cbiagijr@gmail.com>",
  "MD5sum": "b35e052bf1a035f2746326faf955ed0a",
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  "_type": "src",
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  "_created": "2026-05-29T08:33:14.000Z",
  "_published": "2026-05-29T10:24:01.780Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "microarray",
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    "transcription",
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  "_realowner": "bioc",
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    "bivar.awk",
    "CircosTargets",
    "clustCoef",
    "clustCoefPercentage",
    "densityPlot",
    "diffusion",
    "enrichPlot",
    "expDiff",
    "getData",
    "getDE",
    "getEnrich",
    "getGroupGO",
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    "histPlot",
    "InputData",
    "netConditionsPlot",
    "netGOTFPlot",
    "NetworkData",
    "normExp",
    "OutputData",
    "PCIT",
    "pcitC",
    "RIF",
    "RIFPlot",
    "runAnalysis",
    "SmearPlot",
    "tolerance"
  ],
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      "title": "CeTFdemo class object example",
      "object": "CeTFdemo",
      "class": [
        "CeTF"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      ],
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      "table": false,
      "tojson": true
    },
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      "object": "refGenes",
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      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
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      "class": [
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      "title": "Simulated counts data",
      "object": "simCounts",
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      ],
      "fields": [
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        "sample2",
        "sample3",
        "sample4",
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        "array"
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        "cond1",
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      "tojson": true
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      "object": "TFs",
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      "fields": [],
      "table": false,
      "tojson": true
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  "_help": [
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      "page": "bivar.awk",
      "title": "Summary statistics from two variables",
      "topics": [
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    },
    {
      "page": "CeTF-class",
      "title": "The CeTF Class",
      "topics": [
        "CeTF",
        "CeTF-class"
      ]
    },
    {
      "page": "CeTFdemo",
      "title": "CeTFdemo class object example",
      "topics": [
        "CeTFdemo"
      ]
    },
    {
      "page": "CircosTargets",
      "title": "Circos plot for the Transcription Factors/genes targets.",
      "topics": [
        "CircosTargets"
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    },
    {
      "page": "clustCoef",
      "title": "Calculate the clustering coefficient",
      "topics": [
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    },
    {
      "page": "clustCoefPercentage",
      "title": "Calculate the clustering coefficient as a percentage",
      "topics": [
        "clustCoefPercentage"
      ]
    },
    {
      "page": "densityPlot",
      "title": "Density distribution of correlation coefficients and significant PCIT values",
      "topics": [
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    },
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      "page": "diffusion",
      "title": "Network diffusion analysis",
      "topics": [
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      "page": "enrichdemo",
      "title": "Enrichment data",
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      ]
    },
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      "page": "enrichPlot",
      "title": "Plots to visualize the enrichment analysis results",
      "topics": [
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      "page": "expDiff",
      "title": "Differential expression analysis",
      "topics": [
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      "page": "getData-methods",
      "title": "Data accessor for a CeTF class object.",
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        "getData,CeTF-method"
      ]
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      "page": "getDE-methods",
      "title": "Differential Expression accessor for a CeTF class object.",
      "topics": [
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        "getDE,CeTF-method"
      ]
    },
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      "page": "getEnrich",
      "title": "Enrichment analysis for genes of network",
      "topics": [
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      "page": "getGroupGO",
      "title": "Functional Profile of a gene set at specific GO level",
      "topics": [
        "getGroupGO"
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    },
    {
      "page": "gtfToBed",
      "title": "Converts GTF to BED",
      "topics": [
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      ]
    },
    {
      "page": "heatPlot",
      "title": "Heatmap-like functional classification",
      "topics": [
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      "page": "histPlot",
      "title": "Histogram of connectivity distribution",
      "topics": [
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    {
      "page": "InputData-methods",
      "title": "Input data accessor for a CeTF class object.",
      "topics": [
        "InputData",
        "InputData,CeTF-method"
      ]
    },
    {
      "page": "netConditionsPlot",
      "title": "Network plot of gene-gene/gene-TFs interactions",
      "topics": [
        "netConditionsPlot"
      ]
    },
    {
      "page": "netGOTFPlot",
      "title": "Plot a network for Ontologies, genes and TFs",
      "topics": [
        "netGOTFPlot"
      ]
    },
    {
      "page": "NetworkData-methods",
      "title": "Networks data accessor for a CeTF class object.",
      "topics": [
        "NetworkData",
        "NetworkData,CeTF-method"
      ]
    },
    {
      "page": "normExp",
      "title": "Normalized expression transformation",
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      "page": "OutputData-methods",
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      ]
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      "topics": [
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      ]
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      "page": "pcitC",
      "title": "A helper to calculate PCIT implemented in C/C++",
      "topics": [
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      ]
    },
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      "page": "refGenes",
      "title": "List of reference genes for 5 different organisms to perform enrichment",
      "topics": [
        "refGenes"
      ]
    },
    {
      "page": "RIF",
      "title": "Regulatory Impact Factors (RIF) analysis",
      "topics": [
        "RIF"
      ]
    },
    {
      "page": "RIF_input",
      "title": "Regulatory Impact Factors (RIF) input",
      "topics": [
        "RIF_input"
      ]
    },
    {
      "page": "RIFPlot",
      "title": "Relationship plots between RIF1, RIF2 and DE genes",
      "topics": [
        "RIFPlot"
      ]
    },
    {
      "page": "runAnalysis",
      "title": "Whole analysis of Regulatory Impact Factors (RIF) and Partial Correlation and Information Theory analysis (PCIT)",
      "topics": [
        "runAnalysis"
      ]
    },
    {
      "page": "simCounts",
      "title": "Simulated counts data",
      "topics": [
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    },
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      "page": "simNorm",
      "title": "Simulated normalized data",
      "topics": [
        "simNorm"
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    },
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      "page": "SmearPlot",
      "title": "Smear plot for Differentially Expressed genes and TFs",
      "topics": [
        "SmearPlot"
      ]
    },
    {
      "page": "TFs",
      "title": "Transcripition Factors data",
      "topics": [
        "TFs"
      ]
    },
    {
      "page": "tolerance",
      "title": "Tolerance level between 3 pairwise correlations implemented in C/C++",
      "topics": [
        "tolerance"
      ]
    }
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      "title": "Analyzing Regulatory Impact Factors and Partial Correlation and Information Theory",
      "author": "Carlos Alberto Oliveira de Biagi Junior, Ricardo Perecin Nociti, Breno Osvaldo Funicheli, João Paulo Bianchi Ximenez, Patrícia de Cássia Ruy, Marcelo Gomes de Paula, Rafael dos Santos Bezerra and Wilson Araújo da Silva Junior",
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        "Regulatory Information Factors (RIF)",
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        "Installation",
        "Workflow",
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      "modified": "2021-08-10 19:25:51",
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