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  "Package": "metagenomeSeq",
  "Title": "Statistical analysis for sparse high-throughput sequencing",
  "Version": "1.55.0",
  "Date": "2026-04-08",
  "Author": "Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia,\nJustin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo",
  "Maintainer": "Joseph N. Paulson <josephpaulson@gmail.com>",
  "Description": "metagenomeSeq is designed to determine features (be it\nOperational Taxanomic Unit (OTU), species, etc.) that are\ndifferentially abundant between two or more groups of multiple\nsamples. metagenomeSeq is designed to address the effects of\nboth normalization and under-sampling of microbial communities\non disease association detection and the testing of feature\ncorrelations.",
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    "aggregateByTaxonomy",
    "aggSamp",
    "aggTax",
    "biom2MRexperiment",
    "calcNormFactors",
    "calculateEffectiveSamples",
    "correctIndices",
    "correlationTest",
    "cumNorm",
    "cumNormMat",
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    "fitPA",
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    "fitTimeSeries",
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    "libSize",
    "libSize<-",
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    "load_meta",
    "load_metaQ",
    "load_phenoData",
    "loadBiom",
    "loadMeta",
    "loadMetaQ",
    "loadPhenoData",
    "makeLabels",
    "mergeMRexperiments",
    "MRcoefs",
    "MRcounts",
    "MRexperiment2biom",
    "MRfulltable",
    "MRihw",
    "MRtable",
    "newMRexperiment",
    "normFactors",
    "normFactors<-",
    "plotBubble",
    "plotClassTimeSeries",
    "plotCorr",
    "plotFeature",
    "plotGenus",
    "plotMRheatmap",
    "plotOrd",
    "plotOTU",
    "plotRare",
    "plotTimeSeries",
    "posteriorProbs",
    "returnAppropriateObj",
    "ssFit",
    "ssIntervalCandidate",
    "ssPerm",
    "ssPermAnalysis",
    "trapz",
    "ts2MRexperiment",
    "uniqueFeatures",
    "wrenchNorm",
    "zigControl"
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      "title": "OTU abundance matrix of samples from a smoker/non-smoker study",
      "object": "lungData",
      "file": "lungData.rda",
      "class": [
        "MRexperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mouseData",
      "title": "OTU abundance matrix of mice samples from a diet longitudinal study",
      "object": "mouseData",
      "file": "mouseData.rda",
      "class": [
        "MRexperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  "_help": [
    {
      "page": "metagenomeSeq-package",
      "title": "Statistical analysis for sparse high-throughput sequencing",
      "topics": [
        "metagenomeSeq-package",
        "metagenomeSeq"
      ]
    },
    {
      "page": "aggregateBySample",
      "title": "Aggregates a MRexperiment object or counts matrix to by a factor.",
      "topics": [
        "aggregateBySample",
        "aggSamp"
      ]
    },
    {
      "page": "aggregateByTaxonomy",
      "title": "Aggregates a MRexperiment object or counts matrix to a particular level.",
      "topics": [
        "aggregateByTaxonomy",
        "aggTax"
      ]
    },
    {
      "page": "biom2MRexperiment",
      "title": "Biom to MRexperiment objects",
      "topics": [
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      ]
    },
    {
      "page": "calcNormFactors",
      "title": "Cumulative sum scaling (css) normalization factors",
      "topics": [
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      ]
    },
    {
      "page": "calcPosComponent",
      "title": "Positive component",
      "topics": [
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      ]
    },
    {
      "page": "calcShrinkParameters",
      "title": "Calculate shrinkage parameters",
      "topics": [
        "calcShrinkParameters"
      ]
    },
    {
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      "title": "Calculate the zero-inflated log-normal statistic's standard error",
      "topics": [
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      ]
    },
    {
      "page": "calculateEffectiveSamples",
      "title": "Estimated effective samples per feature",
      "topics": [
        "calculateEffectiveSamples"
      ]
    },
    {
      "page": "calcZeroAdjustment",
      "title": "Calculate the zero-inflated component's adjustment factor",
      "topics": [
        "calcZeroAdjustment"
      ]
    },
    {
      "page": "calcZeroComponent",
      "title": "Zero component",
      "topics": [
        "calcZeroComponent"
      ]
    },
    {
      "page": "correctIndices",
      "title": "Calculate the correct indices for the output of correlationTest",
      "topics": [
        "correctIndices"
      ]
    },
    {
      "page": "correlationTest",
      "title": "Correlation of each row of a matrix or MRexperiment object",
      "topics": [
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        "corTest"
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    {
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      "title": "Cumulative sum scaling normalization",
      "topics": [
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      ]
    },
    {
      "page": "cumNormMat",
      "title": "Cumulative sum scaling factors.",
      "topics": [
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    {
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      "title": "Cumulative sum scaling percentile selection",
      "topics": [
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    },
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      "page": "cumNormStatFast",
      "title": "Cumulative sum scaling percentile selection",
      "topics": [
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    {
      "page": "doCountMStep",
      "title": "Compute the Maximization step calculation for features still active.",
      "topics": [
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      ]
    },
    {
      "page": "doEStep",
      "title": "Compute the Expectation step.",
      "topics": [
        "doEStep"
      ]
    },
    {
      "page": "doZeroMStep",
      "title": "Compute the zero Maximization step.",
      "topics": [
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      ]
    },
    {
      "page": "exportMat",
      "title": "Export the normalized MRexperiment dataset as a matrix.",
      "topics": [
        "exportMat",
        "exportMatrix"
      ]
    },
    {
      "page": "exportStats",
      "title": "Various statistics of the count data.",
      "topics": [
        "exportStats"
      ]
    },
    {
      "page": "expSummary",
      "title": "Access MRexperiment object experiment data",
      "topics": [
        "expSummary",
        "expSummary,MRexperiment-method"
      ]
    },
    {
      "page": "extractMR",
      "title": "Extract the essentials of an MRexperiment.",
      "topics": [
        "extractMR"
      ]
    },
    {
      "page": "filterData",
      "title": "Filter datasets according to no. features present in features with at least a certain depth.",
      "topics": [
        "filterData"
      ]
    },
    {
      "page": "fitDO",
      "title": "Wrapper to calculate Discovery Odds Ratios on feature values.",
      "topics": [
        "fitDO"
      ]
    },
    {
      "page": "fitFeatureModel",
      "title": "Computes differential abundance analysis using a zero-inflated log-normal model",
      "topics": [
        "fitFeatureModel"
      ]
    },
    {
      "page": "fitFeatureModelResults-class",
      "title": "Class \"fitFeatureModelResults\" - a formal class for storing results from a fitFeatureModel call",
      "topics": [
        "fitFeatureModelResults-class"
      ]
    },
    {
      "page": "fitLogNormal",
      "title": "Computes a log-normal linear model and permutation based p-values.",
      "topics": [
        "fitLogNormal"
      ]
    },
    {
      "page": "fitMultipleTimeSeries",
      "title": "Discover differentially abundant time intervals for all bacteria",
      "topics": [
        "fitMultipleTimeSeries"
      ]
    },
    {
      "page": "fitPA",
      "title": "Wrapper to run fisher's test on presence/absence of a feature.",
      "topics": [
        "fitPA"
      ]
    },
    {
      "page": "fitSSTimeSeries",
      "title": "Discover differentially abundant time intervals using SS-Anova",
      "topics": [
        "fitSSTimeSeries"
      ]
    },
    {
      "page": "fitTimeSeries",
      "title": "Discover differentially abundant time intervals",
      "topics": [
        "fitTimeSeries"
      ]
    },
    {
      "page": "fitZeroLogNormal",
      "title": "Compute the log fold-change estimates for the zero-inflated log-normal model",
      "topics": [
        "fitZeroLogNormal"
      ]
    },
    {
      "page": "fitZig",
      "title": "Computes the weighted fold-change estimates and t-statistics.",
      "topics": [
        "fitZig"
      ]
    },
    {
      "page": "fitZigResults-class",
      "title": "Class \"fitZigResults\" - a formal class for storing results from a fitZig call",
      "topics": [
        "fitZigResults-class"
      ]
    },
    {
      "page": "getCountDensity",
      "title": "Compute the value of the count density function from the count model residuals.",
      "topics": [
        "getCountDensity"
      ]
    },
    {
      "page": "getEpsilon",
      "title": "Calculate the relative difference between iterations of the negative log-likelihoods.",
      "topics": [
        "getEpsilon"
      ]
    },
    {
      "page": "getNegativeLogLikelihoods",
      "title": "Calculate the negative log-likelihoods for the various features given the residuals.",
      "topics": [
        "getNegativeLogLikelihoods"
      ]
    },
    {
      "page": "getPi",
      "title": "Calculate the mixture proportions from the zero model / spike mass model residuals.",
      "topics": [
        "getPi"
      ]
    },
    {
      "page": "getZ",
      "title": "Calculate the current Z estimate responsibilities (posterior probabilities)",
      "topics": [
        "getZ"
      ]
    },
    {
      "page": "isItStillActive",
      "title": "Function to determine if a feature is still active.",
      "topics": [
        "isItStillActive"
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    },
    {
      "page": "libSize",
      "title": "Access sample depth of coverage from MRexperiment object",
      "topics": [
        "libSize"
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    },
    {
      "page": "libSize-set",
      "title": "Replace the library sizes in a MRexperiment object",
      "topics": [
        "libSize<-",
        "libSize<-,MRexperiment,numeric-method"
      ]
    },
    {
      "page": "loadBiom",
      "title": "Load objects organized in the Biom format.",
      "topics": [
        "loadBiom"
      ]
    },
    {
      "page": "loadMeta",
      "title": "Load a count dataset associated with a study.",
      "topics": [
        "loadMeta",
        "metagenomicLoader"
      ]
    },
    {
      "page": "loadMetaQ",
      "title": "Load a count dataset associated with a study set up in a Qiime format.",
      "topics": [
        "loadMetaQ",
        "qiimeLoader"
      ]
    },
    {
      "page": "loadPhenoData",
      "title": "Load a clinical/phenotypic dataset associated with a study.",
      "topics": [
        "loadPhenoData",
        "phenoData"
      ]
    },
    {
      "page": "lungData",
      "title": "OTU abundance matrix of samples from a smoker/non-smoker study",
      "topics": [
        "lungData"
      ]
    },
    {
      "page": "makeLabels",
      "title": "Function to make labels simpler",
      "topics": [
        "makeLabels"
      ]
    },
    {
      "page": "mergeMRexperiments",
      "title": "Merge two MRexperiment objects together",
      "topics": [
        "mergeMRexperiments"
      ]
    },
    {
      "page": "mergeTable",
      "title": "Merge two tables",
      "topics": [
        "mergeTable"
      ]
    },
    {
      "page": "metagenomeSeq-deprecated",
      "title": "Depcrecated functions in the metagenomeSeq package.",
      "topics": [
        "deprecated_metagenomeSeq_function",
        "fitMeta",
        "load_biom",
        "load_meta",
        "load_metaQ",
        "load_phenoData",
        "metagenomeSeq-deprecated"
      ]
    },
    {
      "page": "mouseData",
      "title": "OTU abundance matrix of mice samples from a diet longitudinal study",
      "topics": [
        "mouseData"
      ]
    },
    {
      "page": "MRcoefs",
      "title": "Table of top-ranked features from fitZig or fitFeatureModel",
      "topics": [
        "MRcoefs"
      ]
    },
    {
      "page": "MRcounts",
      "title": "Accessor for the counts slot of a MRexperiment object",
      "topics": [
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        "MRcounts,MRexperiment-method"
      ]
    },
    {
      "page": "MRexperiment-class",
      "title": "Class \"MRexperiment\" - a modified eSet object for the data from high-throughput sequencing experiments",
      "topics": [
        "colMeans,MRexperiment-method",
        "colSums,MRexperiment-method",
        "libSize,MRexperiment-method",
        "MRexperiment-class",
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      "page": "MRfulltable",
      "title": "Table of top microbial marker gene from linear model fit including sequence information",
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      "page": "plotFeature",
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      "page": "plotGenus",
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    },
    {
      "page": "plotMRheatmap",
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      "page": "plotOTU",
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      "page": "plotRare",
      "title": "Plot of rarefaction effect",
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    {
      "page": "plotTimeSeries",
      "title": "Plot difference function for particular bacteria",
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      "page": "posteriorProbs",
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