{
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  "Package": "fCI",
  "Type": "Package",
  "Title": "f-divergence Cutoff Index for Differential Expression Analysis\nin Transcriptomics and Proteomics",
  "Version": "1.43.0",
  "Date": "2016-02-03",
  "Author": "Shaojun Tang",
  "Maintainer": "Shaojun Tang <tangshao2008@gmail.com>",
  "Description": "(f-divergence Cutoff Index), is to find DEGs in the\ntranscriptomic & proteomic data, and identify DEGs by computing\nthe difference between the distribution of fold-changes for the\ncontrol-control and remaining (non-differential) case-control\ngene expression ratio data. fCI provides several advantages\ncompared to existing methods.",
  "License": "GPL (>= 2)",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:41:27 UTC",
  "RemoteUrl": "https://github.com/bioc/fCI",
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  "_published": "2026-05-30T12:02:26.693Z",
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  "_exports": [
    "call.npci",
    "compute",
    "deg.pairwise.fold.change",
    "deg.up.down.info",
    "deseq.median.ratio.normalization",
    "divergence.multivariate.distributions",
    "fCI.call.by.index",
    "figures",
    "find.fci.targets",
    "find.mid.point",
    "get.fold.large.step",
    "get.npci.data",
    "get.npci.distance.matrix",
    "get.outline.index",
    "get.protein.fold.step",
    "get.rank.combinations",
    "get.rna.fold.step",
    "intersect.of.lists",
    "is.installed",
    "normalization",
    "npci.gene.by.pvalues",
    "npci.index.reconsidered",
    "npci.index.to.be.removed",
    "npci.venn.diagram",
    "pairwise.change.occupancy",
    "populate",
    "report.target.summary",
    "setfCI",
    "show.targets",
    "summarize",
    "total.library.size.normalization",
    "trim.size.normalization",
    "two.sample.log.ratio",
    "two.sample.permutation.test",
    "venndiagram"
  ],
  "_datasets": [
    {
      "name": "fci.data",
      "title": "data frame of gene expression",
      "object": "fci",
      "file": "fci.RData",
      "class": [
        "data.frame"
      ],
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        "A1",
        "A2",
        "A3",
        "B1",
        "B2",
        "B3"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "multi.dimensional.fci.data",
      "title": "data frame of gene expression",
      "object": "multi.dimensional.fci",
      "file": "multi.dimensional.fci.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X2",
        "X4",
        "X18",
        "X24",
        "X7",
        "X4.1",
        "X93",
        "X77"
      ],
      "rows": 14204,
      "table": true,
      "tojson": true
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    {
      "page": "call.npci",
      "title": "the s4 class function",
      "topics": [
        "call.npci"
      ]
    },
    {
      "page": "call.npci-methods",
      "title": "~~ Methods for Function 'call.npci' ~~",
      "topics": [
        "call.npci,NPCI-method",
        "call.npci-methods"
      ]
    },
    {
      "page": "compute",
      "title": "the generic function 'compute' for s4 class",
      "topics": [
        "compute"
      ]
    },
    {
      "page": "compute-methods",
      "title": "~~ Methods for Function 'compute' ~~",
      "topics": [
        "compute,NPCI-method",
        "compute-methods"
      ]
    },
    {
      "page": "deg.pairwise.fold.change",
      "title": "find targets that have a consistent fold change in the same direction (either up- or down-regulation)",
      "topics": [
        "deg.pairwise.fold.change"
      ]
    },
    {
      "page": "deg.up.down.info",
      "title": "find targets and their detailed expression changes",
      "topics": [
        "deg.up.down.info"
      ]
    },
    {
      "page": "deseq.median.ratio.normalization",
      "title": "data matrix normalization method",
      "topics": [
        "deseq.median.ratio.normalization"
      ]
    },
    {
      "page": "divergence.multivariate.distributions",
      "title": "estimate fCI divergence for given samples of aritrary dimensions",
      "topics": [
        "divergence.multivariate.distributions"
      ]
    },
    {
      "page": "fCI-class",
      "title": "Class '\"fCI\"'",
      "topics": [
        "fCI-class"
      ]
    },
    {
      "page": "fCI.call.by.index",
      "title": "top level function call to find targets based on expression data and control & case indexes",
      "topics": [
        "fCI.call.by.index"
      ]
    },
    {
      "page": "fci.data",
      "title": "data frame of gene expression",
      "topics": [
        "fci.data"
      ]
    },
    {
      "page": "figures",
      "title": "generic function to draw figures of the current analysis",
      "topics": [
        "figures"
      ]
    },
    {
      "page": "figures-methods",
      "title": "generate figures for empirical null and case-control distributions",
      "topics": [
        "figures,NPCI-method",
        "figures-methods"
      ]
    },
    {
      "page": "find.fci.targets",
      "title": "identify differentially expressed genes",
      "topics": [
        "find.fci.targets"
      ]
    },
    {
      "page": "find.fci.targets-methods",
      "title": "~~ Methods for Function 'find.fci.targets' ~~",
      "topics": [
        "find.fci.targets,NPCI-method",
        "find.fci.targets-methods"
      ]
    },
    {
      "page": "find.mid.point",
      "title": "find the middle value of the density distribution",
      "topics": [
        "find.mid.point"
      ]
    },
    {
      "page": "get.fold.large.step",
      "title": "generate fold change cutoff values for fCI divergence computation",
      "topics": [
        "get.fold.large.step"
      ]
    },
    {
      "page": "get.npci.data",
      "title": "return a fCI object given the gene expression data",
      "topics": [
        "get.npci.data"
      ]
    },
    {
      "page": "get.npci.distance.matrix",
      "title": "generate the divergence estimation based of fold change cutoff values",
      "topics": [
        "get.npci.distance.matrix"
      ]
    },
    {
      "page": "get.outline.index",
      "title": "find the outline genes of a given distribution",
      "topics": [
        "get.outline.index"
      ]
    },
    {
      "page": "get.protein.fold.step",
      "title": "generate fold-change cutoff on proteomics data (with large steps of 0.2-0.5 fold)",
      "topics": [
        "get.protein.fold.step"
      ]
    },
    {
      "page": "get.rank.combinations",
      "title": "fold change values",
      "topics": [
        "get.rank.combinations"
      ]
    },
    {
      "page": "get.rna.fold.step",
      "title": "generate fCI fold-change cutoff values for typical RNA-Seq data",
      "topics": [
        "get.rna.fold.step"
      ]
    },
    {
      "page": "initialize-methods",
      "title": "~~ Methods for Function 'initialize' ~~",
      "topics": [
        "initialize,NPCI-method",
        "initialize-methods"
      ]
    },
    {
      "page": "intersect.of.lists",
      "title": "find the common values of all vectors of a list",
      "topics": [
        "intersect.of.lists"
      ]
    },
    {
      "page": "is.installed",
      "title": "package",
      "topics": [
        "is.installed"
      ]
    },
    {
      "page": "multi.dimensional.fci.data",
      "title": "data frame of gene expression",
      "topics": [
        "multi.dimensional.fci.data"
      ]
    },
    {
      "page": "normalization",
      "title": "generic function to normalize gene expression matrix",
      "topics": [
        "normalization"
      ]
    },
    {
      "page": "normalization-methods",
      "title": "~~ Methods for Function 'normalization' ~~",
      "topics": [
        "normalization,NPCI-method",
        "normalization-methods"
      ]
    },
    {
      "page": "NPCI-class",
      "title": "Class '\"NPCI\"'",
      "topics": [
        "NPCI-class"
      ]
    },
    {
      "page": "npci.gene.by.pvalues",
      "title": "find most signficantly change fCI targets",
      "topics": [
        "npci.gene.by.pvalues"
      ]
    },
    {
      "page": "npci.index.reconsidered",
      "title": "find targets that have little evidence to be differentially expressed",
      "topics": [
        "npci.index.reconsidered"
      ]
    },
    {
      "page": "npci.index.to.be.removed",
      "title": "gene indexes that will be considered as targets",
      "topics": [
        "npci.index.to.be.removed"
      ]
    },
    {
      "page": "npci.venn.diagram",
      "title": "generate venn diagram for multiple fCI analysis",
      "topics": [
        "npci.venn.diagram"
      ]
    },
    {
      "page": "pairwise.change.occupancy",
      "title": "find the targets whose fold changes occur consistently (upregulated or downregulated) in all fCI analysis",
      "topics": [
        "pairwise.change.occupancy"
      ]
    },
    {
      "page": "populate",
      "title": "generic function to populate the fCI object based on provided data",
      "topics": [
        "populate"
      ]
    },
    {
      "page": "populate-methods",
      "title": "~~ Methods for Function 'populate' ~~",
      "topics": [
        "populate,NPCI-method",
        "populate-methods"
      ]
    },
    {
      "page": "report.target.summary",
      "title": "generate the results (gene ids) in the data frame",
      "topics": [
        "report.target.summary"
      ]
    },
    {
      "page": "setfCI",
      "title": "the generic function 'setfCI' for s4 class",
      "topics": [
        "setfCI"
      ]
    },
    {
      "page": "setfCI-methods",
      "title": "~~ Methods for Function 'setfCI' ~~",
      "topics": [
        "setfCI,NPCI-method",
        "setfCI-methods"
      ]
    },
    {
      "page": "show.targets",
      "title": "display the gene ids that are identified to be differentially regulated",
      "topics": [
        "show.targets"
      ]
    },
    {
      "page": "show.targets-methods",
      "title": "~~ Methods for Function 'show.targets' ~~",
      "topics": [
        "show.targets,NPCI-method",
        "show.targets-methods"
      ]
    },
    {
      "page": "summarize",
      "title": "result summerization",
      "topics": [
        "summarize"
      ]
    },
    {
      "page": "summarize-methods",
      "title": "result summerization",
      "topics": [
        "summarize,NPCI-method",
        "summarize-methods"
      ]
    },
    {
      "page": "total.library.size.normalization",
      "title": "normalize the gene expression based on the library size (summation) of the first sample replicate",
      "topics": [
        "total.library.size.normalization"
      ]
    },
    {
      "page": "trim.size.normalization",
      "title": "normalize gene expression by exluding genes on the top 5 and bottom 5 percentage",
      "topics": [
        "trim.size.normalization"
      ]
    },
    {
      "page": "two.sample.log.ratio",
      "title": "compute the log ratios of two vectors",
      "topics": [
        "two.sample.log.ratio"
      ]
    },
    {
      "page": "two.sample.permutation.test",
      "title": "perform permuation test on two vectors",
      "topics": [
        "two.sample.permutation.test"
      ]
    },
    {
      "page": "venndiagram",
      "title": "generate a venn diagram to show the differentially expression summaries accross pairwise fCI analysis",
      "topics": [
        "venndiagram"
      ]
    },
    {
      "page": "venndiagram-methods",
      "title": "~~ Methods for Function 'venndiagram' ~~",
      "topics": [
        "venndiagram,NPCI-method",
        "venndiagram-methods"
      ]
    }
  ],
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  "_vignettes": [
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      "source": "fCI.Rmd",
      "filename": "fCI.html",
      "title": "fCI",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to fCI",
        "Authors and Affliations",
        "Abstract",
        "Introduction",
        "Installing fCI",
        "Differential Expression Analysis using fCI",
        "Reading the input data:",
        "Integer raw read counts from NGS data or Spectrum counts from proteomics data",
        "Normalized gene expression such as RPKM or FPKM, or peak intesntiy (height/area) in proteomics data",
        "Ratio data from many experiments measuring relative gene expression with respect to control channels.",
        "Data normalization",
        "Total library normalization",
        "Trimed sum normalization",
        "Kernel density distribution centering",
        "fCI analysis with the Spike-in microarray data",
        "fCI DEG analysis Output",
        "Print Differentially Expressed Genes",
        "The Kernel Density Plot of Control-Control and Control-Case distributions",
        "Alternative function to find DEGs",
        "Testing fCI on a randomly generated simulated dataset",
        "Finding Differentially Expressed Genes (no DEGs in this case):",
        "Multi-dimensional (i.e.Pproteogenomics data) fCI analysis",
        "Example of integrated proteogeonomics analysis",
        "Specifying fCI runtime variables",
        "Use only transcriptomics dataset in the proteogenomics data",
        "Theory behind fCI"
      ],
      "created": "2015-06-17 08:48:14",
      "modified": "2018-08-30 17:48:32",
      "commits": 7
    }
  ],
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  "_indexed": true,
  "_nocasepkg": "fci",
  "_universes": [
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