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  "Package": "DSS",
  "Title": "Dispersion shrinkage for sequencing data",
  "Version": "2.61.0",
  "Date": "2026-4-9",
  "Author": "Hao Wu<hao.wu@emory.edu>, Hao Feng<hxf155@case.edu>",
  "Maintainer": "Hao Wu <hao.wu@emory.edu>, Hao Feng <hxf155@case.edu>",
  "Description": "DSS is an R library performing differntial analysis for\ncount-based sequencing data. It detectes differentially\nexpressed genes (DEGs) from RNA-seq, and differentially\nmethylated loci or regions (DML/DMRs) from bisulfite sequencing\n(BS-seq). The core of DSS is a new dispersion shrinkage method\nfor estimating the dispersion parameter from Gamma-Poisson or\nBeta-Binomial distributions.",
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  "VignetteBuilder": "knitr",
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    "description": "Distinguished Professor in Artificial Intelligence ",
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    "dispersion",
    "dispersion<-",
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    "DMLtest",
    "DMLtest.multiFactor",
    "DSS.DE",
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    "estNormFactors",
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    "normalizationFactor",
    "normalizationFactor<-",
    "showOneDMR",
    "waldTest"
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      "title": "Experimental design for the example RRBS dataset",
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        "cell"
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      "name": "RRBS",
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      ],
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      "table": false,
      "tojson": false
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      ],
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      "table": false,
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      "page": "DSS-package",
      "title": "Dispersion shrinkage for sequencing data",
      "topics": [
        "DSS-package",
        "DSS"
      ]
    },
    {
      "page": "callDML",
      "title": "Function to detect differntially methylated loci (DML) from bisulfite sequencing (BS-seq) data.",
      "topics": [
        "callDML"
      ]
    },
    {
      "page": "callDMR",
      "title": "Function to detect differntially methylated regions (DMR) from bisulfite sequencing (BS-seq) data.",
      "topics": [
        "callDMR"
      ]
    },
    {
      "page": "design",
      "title": "Experimental design for the example RRBS dataset",
      "topics": [
        "design"
      ]
    },
    {
      "page": "dispersion",
      "title": "Acessor functions for the 'dispersion' slot in a SeqCountData object.",
      "topics": [
        "dispersion",
        "dispersion,SeqCountSet-method",
        "dispersion<-",
        "dispersion<-,SeqCountSet,numeric-method"
      ]
    },
    {
      "page": "DMLfit.multiFactor",
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      "topics": [
        "DMLfit.multiFactor"
      ]
    },
    {
      "page": "DMLtest",
      "title": "Function to perform statistical test of differntially methylated loci (DML) for two group comparisons of bisulfite sequencing (BS-seq) data.",
      "topics": [
        "DMLtest"
      ]
    },
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      "page": "DMLtest.multiFactor",
      "title": "Perform statistical test for BS-seq data from general experimental design",
      "topics": [
        "DMLtest.multiFactor"
      ]
    },
    {
      "page": "DSS.DE",
      "title": "Perform RNA-seq differential expression analysis in two-group comparison",
      "topics": [
        "DSS.DE"
      ]
    },
    {
      "page": "estDispersion",
      "title": "Estimate and shrink tag-specific dipsersions",
      "topics": [
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        "estDispersion,SeqCountSet-method"
      ]
    },
    {
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      "title": "Estimate normalization factors",
      "topics": [
        "estNormFactors",
        "estNormFactors,SeqCountSet-method"
      ]
    },
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      "title": "Create an object of BSseq class from several data frames.",
      "topics": [
        "makeBSseqData"
      ]
    },
    {
      "page": "normalizationFactor",
      "title": "Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.",
      "topics": [
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        "normalizationFactor,SeqCountSet-method",
        "normalizationFactor<-",
        "normalizationFactor<-,SeqCountSet,matrix-method",
        "normalizationFactor<-,SeqCountSet,numeric-method"
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    {
      "page": "RRBS",
      "title": "An example dataset for multiple factor design",
      "topics": [
        "RRBS"
      ]
    },
    {
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      "title": "Class '\"SeqCountSet\"' - container for count data from sequencing experiment",
      "topics": [
        "newSeqCountSet",
        "SeqCountSet",
        "SeqCountSet-class"
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    },
    {
      "page": "seqData",
      "title": "A simulated 'SeqCountData' object.",
      "topics": [
        "seqData"
      ]
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      "title": "Visualze the count data for one DMR",
      "topics": [
        "showOneDMR"
      ]
    },
    {
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      "title": "Perform gene-wise Wald test for two group comparisons for sequencing count data.",
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        "waldTest,SeqCountSet-method"
      ]
    }
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      "title": "The DSS User's Guide",
      "author": "Hao Wu, hao.wu@emory.edu",
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        "Background",
        "Citation",
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        "Input data preparation",
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        "Using DSS for BS-seq differential methylation analysis",
        "Overview",
        "DML/DMR detection from two-group comparison",
        "Parallel computing for DML/DMR detection from two-group comparison",
        "DML/DMR detection from general experimental design",
        "Hypothesis testing in general experimental design",
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      "modified": "2022-08-02 13:02:15",
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      "date": "2026-06-23T15:45:29.000Z",
      "arch": "x86_64",
      "commit": "8a73abe69f82ff677690ac6ef7868eb585ee3242",
      "fileid": "d8332bf1c726fdb343ec6319d65f4c57ebb4024fdcfd026ac558714b34c70aba",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28037621699"
    }
  ]
}