{
  "_id": "6a1af0d51d7bb097a09f6af9",
  "Package": "sSeq",
  "Type": "Package",
  "Title": "Shrinkage estimation of dispersion in Negative Binomial models\nfor RNA-seq experiments with small sample size",
  "Version": "1.51.0",
  "Date": "2013-04-17",
  "Author": "Danni Yu <dyu@purdue.edu>, Wolfgang Huber <whuber@embl.de> and\nOlga Vitek <ovitek@purdue.edu>",
  "Maintainer": "Danni Yu <dyu@purdue.edu>",
  "Description": "The purpose of this package is to discover the genes that\nare differentially expressed between two conditions in RNA-seq\nexperiments. Gene expression is measured in counts of\ntranscripts and modeled with the Negative Binomial (NB)\ndistribution using a shrinkage approach for dispersion\nestimation. The method of moment (MM) estimates for dispersion\nare shrunk towards an estimated target, which minimizes the\naverage squared difference between the shrinkage estimates and\nthe initial estimates. The exact per-gene probability under the\nNB model is calculated, and used to test the hypothesis that\nthe expected expression of a gene in two conditions identically\nfollow a NB distribution.",
  "License": "GPL (>= 3)",
  "LazyLoad": "yes",
  "biocViews": "ImmunoOncology, RNASeq",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:37:42 UTC",
  "RemoteUrl": "https://github.com/bioc/sSeq",
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  "NeedsCompilation": "no",
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    "User": "root"
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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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    "email": "dyu@purdue.edu"
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    "rnaseq"
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "getT",
    "getTgroup",
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    "nbTestSH",
    "plotDispersion",
    "rnbinomMV",
    "rowVars",
    "sim"
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      "name": "countsTable",
      "title": "An Example Simulation Data",
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        "array"
      ],
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    },
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      "title": "An Example Simulation Data",
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      ],
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        "T51"
      ],
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    }
  ],
  "_help": [
    {
      "page": "sSeq-package",
      "title": "Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size",
      "topics": [
        "sSeq-package",
        "sSeq"
      ]
    },
    {
      "page": "countsTable",
      "title": "An Example Simulation Data",
      "topics": [
        "countsTable"
      ]
    },
    {
      "page": "drawMA_vol",
      "title": "Draw MA Plot and Volcano Plot",
      "topics": [
        "drawMA_vol"
      ]
    },
    {
      "page": "ecdfAUC",
      "title": "Draw Empirical Cumulative Density Function (ECDF) plot",
      "topics": [
        "ecdfAUC"
      ]
    },
    {
      "page": "equalSpace",
      "title": "Calculate Grouped Shrinkage Estimates",
      "topics": [
        "equalSpace"
      ]
    },
    {
      "page": "exactNBtest1",
      "title": "Perform only one exact test under the Negative Binomial modeling.",
      "topics": [
        "exactNBtest1"
      ]
    },
    {
      "page": "getAdjustDisp",
      "title": "Calculate Shrinkage (SH) Estimates for Dispersion",
      "topics": [
        "getAdjustDisp"
      ]
    },
    {
      "page": "getNormFactor",
      "title": "Estimate size factors",
      "topics": [
        "getNormFactor"
      ]
    },
    {
      "page": "getQ",
      "title": "Estimate the shrinkage target based on the quantiles of initial targets",
      "topics": [
        "getQ"
      ]
    },
    {
      "page": "getT",
      "title": "Estimate the shrinkage target based on the initial estimates",
      "topics": [
        "getT"
      ]
    },
    {
      "page": "getTgroup",
      "title": "This is an internal function used to calculate the shrinkage estimation when multiple shrinkage targets are considered.",
      "topics": [
        "getTgroup"
      ]
    },
    {
      "page": "Hammer2months",
      "title": "An example of real experiment.",
      "topics": [
        "Hammer2months"
      ]
    },
    {
      "page": "nbinomTestForMatricesSH",
      "title": "Exact test under Negative Binomial Test with Shrinkage Estimates on Dispersions",
      "topics": [
        "nbinomTestForMatricesSH"
      ]
    },
    {
      "page": "nbTestSH",
      "title": "Differential Analysis based on RNA-seq experiments using Negative Binomial (NB) Model with Shrinkage Approach of Dispersion Estimation.",
      "topics": [
        "nbTestSH"
      ]
    },
    {
      "page": "plotDispersion",
      "title": "Drawing Dispersion-Mean plot.",
      "topics": [
        "plotDispersion"
      ]
    },
    {
      "page": "rnbinomMV",
      "title": "Randomly Generate Negative Binomial Variable with parameters mean and variance.",
      "topics": [
        "rnbinomMV"
      ]
    },
    {
      "page": "rowVars",
      "title": "Calculating the sample variance within each row of A matrix",
      "topics": [
        "rowVars"
      ]
    },
    {
      "page": "sim",
      "title": "Generating Simulated Data",
      "topics": [
        "sim"
      ]
    },
    {
      "page": "Sultan",
      "title": "An example of real experiment.",
      "topics": [
        "Sultan"
      ]
    },
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      ]
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      "created": "2013-11-01 20:30:19",
      "modified": "2013-11-01 20:30:19",
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