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  "Title": "Tools for Normalizing and Comparing ChIP-seq Samples",
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  "Description": "Chromatin immunoprecipitation followed by high-throughput\nsequencing (ChIP-seq) is the premier technology for profiling\ngenome-wide localization of chromatin-binding proteins,\nincluding transcription factors and histones with various\nmodifications. This package provides a robust method for\nnormalizing ChIP-seq signals across individual samples or\ngroups of samples. It also designs a self-contained system of\nstatistical models for calling differential ChIP-seq signals\nbetween two or more biological conditions as well as for\ncalling hypervariable ChIP-seq signals across samples. Refer to\nTu et al. (2021) <doi:10.1101/gr.262675.120> and Chen et al.\n(2022) <doi:10.1186/s13059-022-02627-9> for associated\nstatistical details.",
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  "BugReports": "https://github.com/tushiqi/MAnorm2/issues",
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    "cmbBioCond",
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    "diffTest.bioCond",
    "distBioCond",
    "estimatePriorDf",
    "estimatePriorDfRobust",
    "estimateSizeFactors",
    "estimateVarRatio",
    "estParamHyperChIP",
    "extendMeanVarCurve",
    "fitMeanVarCurve",
    "inv.trigamma",
    "isSymPosDef",
    "MAplot",
    "MAplot.bioCond",
    "MAplot.default",
    "MAplot.diffBioCond",
    "mean_var_logwinf",
    "normalize",
    "normalizeBySizeFactors",
    "normBioCond",
    "normBioCondBySizeFactors",
    "plot.aovBioCond",
    "plot.matrix",
    "plot.varTestBioCond",
    "plotMeanVarCurve",
    "plotMVC",
    "print.bioCond",
    "print.summaryBioCond",
    "setMeanVarCurve",
    "setPriorDf",
    "setPriorDfRobust",
    "setPriorDfVarRatio",
    "setWeight",
    "summary.bioCond",
    "util.trigamma",
    "varRatio",
    "varTestBioCond",
    "vstBioCond"
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      "class": [
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      ],
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        "start",
        "end",
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        "GM12891_H3K27Ac_2.read_cnt",
        "GM12892_H3K27Ac_1.read_cnt",
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        "GM12891_H3K27Ac_1.occupancy",
        "GM12891_H3K27Ac_2.occupancy",
        "GM12892_H3K27Ac_1.occupancy",
        "GM12892_H3K27Ac_2.occupancy"
      ],
      "rows": 73828,
      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "aovBioCond",
      "title": "Perform a Moderated Analysis of Variance on 'bioCond' Objects",
      "topics": [
        "aovBioCond"
      ]
    },
    {
      "page": "bioCond",
      "title": "Create a 'bioCond' Object to Group ChIP-seq Samples",
      "topics": [
        "bioCond"
      ]
    },
    {
      "page": "checkCountTable",
      "title": "Check the Regularity of a Count Table",
      "topics": [
        "checkCountTable"
      ]
    },
    {
      "page": "checkIndex",
      "title": "Check the Validity of an Index Vector",
      "topics": [
        "checkIndex"
      ]
    },
    {
      "page": "cmbBioCond",
      "title": "Combine a Set of 'bioCond' Objects into a Single 'bioCond'",
      "topics": [
        "cmbBioCond"
      ]
    },
    {
      "page": "diffTest",
      "title": "Generic Differential Test",
      "topics": [
        "diffTest",
        "diffTest.bioCond"
      ]
    },
    {
      "page": "distBioCond",
      "title": "Quantify the Distance between Each Pair of Samples in a 'bioCond'",
      "topics": [
        "distBioCond"
      ]
    },
    {
      "page": "estimateD0",
      "title": "Workhorse Function for Estimating Number of Prior Degrees of Freedom",
      "topics": [
        "estimateD0"
      ]
    },
    {
      "page": "estimateD0Robust",
      "title": "Estimate Number of Prior Degrees of Freedom in a Robust Manner",
      "topics": [
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      ]
    },
    {
      "page": "estimatePriorDf",
      "title": "Assess the Goodness of Fit of Mean-Variance Curves",
      "topics": [
        "estimatePriorDf"
      ]
    },
    {
      "page": "estimatePriorDfRobust",
      "title": "Assess the Goodness of Fit of Mean-Variance Curves in a Robust Manner",
      "topics": [
        "estimatePriorDfRobust"
      ]
    },
    {
      "page": "estimateSizeFactors",
      "title": "Estimate Size Factors of ChIP-seq Samples",
      "topics": [
        "estimateSizeFactors"
      ]
    },
    {
      "page": "estimateVarRatio",
      "title": "Estimate Relative Variance Ratio Factors of 'bioCond' Objects",
      "topics": [
        "estimateVarRatio"
      ]
    },
    {
      "page": "estParamHyperChIP",
      "title": "The Parameter Estimation Framework of HyperChIP",
      "topics": [
        "estParamHyperChIP"
      ]
    },
    {
      "page": "extendMeanVarCurve",
      "title": "Extend the Application Scope of a Mean-Variance Curve",
      "topics": [
        "extendMeanVarCurve"
      ]
    },
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      "page": "fitMeanVarCurve",
      "title": "Fit a Mean-Variance Curve",
      "topics": [
        "fitMeanVarCurve"
      ]
    },
    {
      "page": "H3K27Ac",
      "title": "ChIP-seq Samples for H3K27Ac in Human Lymphoblastoid Cell Lines",
      "topics": [
        "H3K27Ac"
      ]
    },
    {
      "page": "intervalMeans",
      "title": "Deduce the Sample Mean Signal Intensity",
      "topics": [
        "intervalMeans"
      ]
    },
    {
      "page": "intervalVars",
      "title": "Sample Variance of Replicated Signal Intensities",
      "topics": [
        "intervalVars"
      ]
    },
    {
      "page": "inv.trigamma",
      "title": "Inversion of Trigamma Function",
      "topics": [
        "inv.trigamma"
      ]
    },
    {
      "page": "isSymPosDef",
      "title": "Is a Real Matrix Symmetric and Positive Definite?",
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        "isSymPosDef"
      ]
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    {
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      "title": "Deduce Pearson Correlation Coefficient between M & A Values",
      "topics": [
        "MA.pcc"
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    },
    {
      "page": "MAnorm2",
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      "topics": [
        "MAnorm2"
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      "topics": [
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        "MAplot.default"
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      "topics": [
        "MAplot.diffBioCond"
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    },
    {
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    {
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    {
      "page": "meanVarParaFit",
      "title": "Parametrically Fit a Mean-Variance Curve",
      "topics": [
        "meanVarParaFit"
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    },
    {
      "page": "mvcID.new",
      "title": "Create a New Unique ID for a Mean-Variance Curve",
      "topics": [
        "mvcID.new"
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    },
    {
      "page": "normalize",
      "title": "Perform MA Normalization on a Set of ChIP-seq Samples",
      "topics": [
        "normalize"
      ]
    },
    {
      "page": "normalizeBySizeFactors",
      "title": "Normalize ChIP-seq Samples by Their Size Factors",
      "topics": [
        "normalizeBySizeFactors"
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    },
    {
      "page": "normBioCond",
      "title": "Perform MA Normalization on a Set of 'bioCond' Objects",
      "topics": [
        "normBioCond"
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    },
    {
      "page": "normBioCondBySizeFactors",
      "title": "Normalize 'bioCond' Objects by Their Size Factors",
      "topics": [
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    },
    {
      "page": "normCoef",
      "title": "Deduce MA Normalization Coefficients",
      "topics": [
        "normCoef"
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    },
    {
      "page": "plot.aovBioCond",
      "title": "Plot an 'aovBioCond' Object",
      "topics": [
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    {
      "page": "plot.matrix",
      "title": "Visualize a Matrix of Numeric Values",
      "topics": [
        "plot.matrix"
      ]
    },
    {
      "page": "plot.varTestBioCond",
      "title": "Plot a 'varTestBioCond' Object",
      "topics": [
        "plot.varTestBioCond"
      ]
    },
    {
      "page": "plotMeanVarCurve",
      "title": "Plot a Mean-Variance Curve",
      "topics": [
        "plotMeanVarCurve"
      ]
    },
    {
      "page": "plotMVC",
      "title": "Plot a Mean-Variance Curve on a Single 'bioCond' Object",
      "topics": [
        "plotMVC"
      ]
    },
    {
      "page": "print.bioCond",
      "title": "Print a 'bioCond' Object",
      "topics": [
        "print.bioCond"
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    },
    {
      "page": "print.summaryBioCond",
      "title": "Print a 'summaryBioCond' Object",
      "topics": [
        "print.summaryBioCond"
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    },
    {
      "page": "scaleMeanVarCurve",
      "title": "Scale a Mean-Variance Curve",
      "topics": [
        "scaleMeanVarCurve"
      ]
    },
    {
      "page": "scaleMeanVarCurveRobust",
      "title": "Scale a Mean-Variance Curve in a Robust Manner",
      "topics": [
        "scaleMeanVarCurveRobust"
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    },
    {
      "page": "setMeanVarCurve",
      "title": "Set the Mean-Variance Curve of a Set of 'bioCond' Objects",
      "topics": [
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    },
    {
      "page": "setPriorDf",
      "title": "Set the Number of Prior Degrees of Freedom of Mean-Variance Curves",
      "topics": [
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      ]
    },
    {
      "page": "setPriorDfRobust",
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      "topics": [
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    },
    {
      "page": "setPriorDfVarRatio",
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      "page": "setWeight",
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      "page": "summary.bioCond",
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      "title": "Call Hypervariable and Invariant Intervals for a 'bioCond'",
      "topics": [
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    {
      "page": "vstBioCond",
      "title": "Apply a Variance-Stabilizing Transformation to a 'bioCond'",
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      "title": "MAnorm2 for Normalizing and Comparing ChIP-seq Samples",
      "author": "Shiqi Tu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "The System of MAnorm2 Machinery",
        "Input Data",
        "Application Scope",
        "Continuous Distribution",
        "MAnorm2 Capability",
        "Comparing Groups of ChIP-seq Samples",
        "Quick Start",
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        "Normalization",
        "Modeling Mean-Variance Trend",
        "Differential Tests",
        "When No Replicates Are Available",
        "Simultaneous Comparison of Any Number of Groups",
        "Combining Replicates and Using Local Regression",
        "Identifying Hypervariable ChIP-seq Signals",
        "Clustering ChIP-seq Samples",
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        "Citation",
        "Acknowledgments",
        "Session Info",
        "References"
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      "created": "2020-01-09 13:40:00",
      "modified": "2022-10-31 08:49:19",
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