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    "varianceStabilizingTransformation",
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      "title": "DESeq2 package for differential analysis of count data",
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        "DESeq2"
      ]
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    {
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    {
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    },
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        "counts<-,DESeqDataSet,matrix-method"
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      "title": "Differential expression analysis based on the Negative Binomial (a.k.a. Gamma-Poisson) distribution",
      "topics": [
        "DESeq"
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    {
      "page": "DESeqDataSet",
      "title": "DESeqDataSet object and constructors",
      "topics": [
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        "DESeqDataSet-class",
        "DESeqDataSetFromHTSeqCount",
        "DESeqDataSetFromMatrix",
        "DESeqDataSetFromTximport"
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      "topics": [
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        "DESeqResults-class"
      ]
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      "title": "DESeqTransform object and constructor",
      "topics": [
        "DESeqTransform",
        "DESeqTransform-class"
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    },
    {
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      "title": "Accessors for the 'design' slot of a DESeqDataSet object.",
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        "design<-,DESeqDataSet,formula-method",
        "design<-,DESeqDataSet,matrix-method"
      ]
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    {
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      "title": "Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.",
      "topics": [
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        "dispersionFunction,DESeqDataSet-method",
        "dispersionFunction<-",
        "dispersionFunction<-,DESeqDataSet,function-method"
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      "topics": [
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        "dispersions,DESeqDataSet-method",
        "dispersions<-",
        "dispersions<-,DESeqDataSet,numeric-method"
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        "estimateMLEForBetaPriorVar"
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      ]
    },
    {
      "page": "estimateDispersionsGeneEst",
      "title": "Low-level functions to fit dispersion estimates",
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        "estimateDispersionsGeneEst",
        "estimateDispersionsMAP",
        "estimateDispersionsPriorVar"
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    {
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      "title": "FPM: fragments per million mapped fragments",
      "topics": [
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      "title": "Shrink log2 fold changes",
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      "topics": [
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      "title": "Accessor functions for the normalization factors in a DESeqDataSet object.",
      "topics": [
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        "normalizationFactors,DESeqDataSet-method",
        "normalizationFactors<-",
        "normalizationFactors<-,DESeqDataSet,matrix-method"
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      "title": "Normalize for gene length",
      "topics": [
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      "topics": [
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      "topics": [
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      "title": "Plot dispersion estimates",
      "topics": [
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        "plotDispEsts,DESeqDataSet-method"
      ]
    },
    {
      "page": "plotMA",
      "title": "MA-plot from base means and log fold changes",
      "topics": [
        "plotMA",
        "plotMA,DESeqDataSet-method",
        "plotMA,DESeqResults-method"
      ]
    },
    {
      "page": "plotPCA",
      "title": "Sample PCA plot for transformed data",
      "topics": [
        "plotPCA",
        "plotPCA,DESeqTransform-method"
      ]
    },
    {
      "page": "plotSparsity",
      "title": "Sparsity plot",
      "topics": [
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      ]
    },
    {
      "page": "priorInfo",
      "title": "Accessors for the 'priorInfo' slot of a DESeqResults object.",
      "topics": [
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        "priorInfo<-",
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      "page": "replaceOutliers",
      "title": "Replace outliers with trimmed mean",
      "topics": [
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        "replaceOutliersWithTrimmedMean"
      ]
    },
    {
      "page": "results",
      "title": "Extract results from a DESeq analysis",
      "topics": [
        "removeResults",
        "results",
        "resultsNames"
      ]
    },
    {
      "page": "rlog",
      "title": "Apply a 'regularized log' transformation",
      "topics": [
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        "rlogTransformation"
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    },
    {
      "page": "show",
      "title": "Show method for DESeqResults objects",
      "topics": [
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      "page": "sizeFactors",
      "title": "Accessor functions for the 'sizeFactors' information in a DESeqDataSet object.",
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        "unmix"
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      "title": "Apply a variance stabilizing transformation (VST) to the count data",
      "topics": [
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        "varianceStabilizingTransformation"
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      "source": "DESeq2.Rmd",
      "filename": "DESeq2.html",
      "title": "Analyzing RNA-seq data with DESeq2",
      "author": "Michael I. Love, Simon Anders, and Wolfgang Huber",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Standard workflow",
        "Quick start",
        "How to get help for DESeq2",
        "Acknowledgments",
        "Funding",
        "Input data",
        "Why un-normalized counts?",
        "The DESeqDataSet",
        "Transcript abundance files and tximport / tximeta",
        "Tximeta for import with automatic metadata",
        "Count matrix input",
        "htseq-count input",
        "SummarizedExperiment input",
        "Pre-filtering",
        "Note on factor levels",
        "Collapsing technical replicates",
        "About the pasilla dataset",
        "Differential expression analysis",
        "Log fold change shrinkage for visualization and ranking",
        "Speed-up and parallelization thoughts",
        "p-values and adjusted p-values",
        "Independent hypothesis weighting",
        "Exploring and exporting results",
        "MA-plot",
        "Alternative shrinkage estimators",
        "Plot counts",
        "More information on results columns",
        "Rich visualization and reporting of results",
        "Exporting results to CSV files",
        "Multi-factor designs",
        "Data transformations and visualization",
        "Count data transformations",
        "Blind dispersion estimation",
        "Extracting transformed values",
        "Variance stabilizing transformation",
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        "Effects of transformations on the variance",
        "Data quality assessment by sample clustering and visualization",
        "Heatmap of the count matrix",
        "Heatmap of the sample-to-sample distances",
        "Principal component plot of the samples",
        "Variations to the standard workflow",
        "Wald test individual steps",
        "Control features for estimating size factors",
        "Contrasts",
        "Interactions",
        "Time-series experiments",
        "Likelihood ratio test",
        "Extended section on shrinkage estimators",
        "Recommendations for single-cell analysis",
        "Approach to count outliers",
        "Dispersion plot and fitting alternatives",
        "Local or mean dispersion fit",
        "Supply a custom dispersion fit",
        "Independent filtering of results",
        "Tests of log2 fold change above or below a threshold",
        "Access to all calculated values",
        "Sample-/gene-dependent normalization factors",
        "\"Model matrix not full rank\"",
        "Linear combinations",
        "Group-specific condition effects, individuals nested within groups",
        "Levels without samples",
        "Theory behind DESeq2",
        "The DESeq2 model",
        "Changes compared to DESeq",
        "Methods changes since the 2014 DESeq2 paper",
        "Count outlier detection",
        "Expanded model matrices",
        "Independent filtering and multiple testing",
        "Filtering criteria",
        "Why does it work?",
        "Frequently asked questions",
        "How can I get support for DESeq2?",
        "Why are some p values set to NA?",
        "How can I get unfiltered DESeq2 results?",
        "How do I use VST or rlog data for differential testing?",
        "Why after VST are there still batches in the PCA plot?",
        "Do normalized counts correct for variables in the design?",
        "Can I use DESeq2 to analyze paired samples?",
        "If I have multiple groups, should I run all together or split into pairs of groups?",
        "Can I run DESeq2 to contrast the levels of many groups?",
        "Can I use DESeq2 to analyze a dataset without replicates?",
        "How can I include a continuous covariate in the design formula?",
        "I ran a likelihood ratio test, but results() only gives me one comparison.",
        "What are the exact steps performed by DESeq()?",
        "Is there an official Galaxy tool for DESeq2?",
        "I want to benchmark DESeq2 comparing to other DE tools.",
        "I have trouble installing DESeq2 on Ubuntu/Linux...",
        "Session info",
        "References"
      ],
      "created": "2016-11-18 04:43:20",
      "modified": "2025-11-18 13:51:50",
      "commits": 130
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