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  "Version": "4.11.1",
  "Date": "2026-05-23",
  "Title": "Empirical Analysis of Digital Gene Expression Data in R",
  "Description": "Differential expression analysis of sequence count data.\nImplements a range of statistical methodology based on the\nnegative binomial distributions, including empirical Bayes\nestimation, exact tests, generalized linear models,\nquasi-likelihood, and gene set enrichment. Can perform\ndifferential analyses of any type of omics data that produces\nread counts, including RNA-seq, ChIP-seq, ATAC-seq,\nBisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral\ncounts. RNA-seq analyses can be conducted at the gene or\nisoform level, and tests can be conducted for differential exon\nor transcript usage.",
  "Author": "Yunshun Chen, Lizhong Chen, Aaron TL Lun, Davis J McCarthy,\nPedro Baldoni, Matthew E Ritchie, Belinda Phipson, Yifang Hu,\nXiaobei Zhou, Mark D Robinson, Gordon K Smyth",
  "Maintainer": "Yunshun Chen <yuchen@wehi.edu.au>, Gordon Smyth\n<smyth@wehi.edu.au>, Aaron Lun\n<infinite.monkeys.with.keyboards@gmail.com>, Mark Robinson\n<mark.robinson@imls.uzh.ch>",
  "License": "GPL (>=2)",
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  "URL": "https://bioinf.wehi.edu.au/edgeR/,\nhttps://bioconductor.org/packages/edgeR",
  "biocViews": "AlternativeSplicing, BatchEffect, Bayesian,\nBiomedicalInformatics, CellBiology, ChIPSeq, Clustering,\nCoverage, DifferentialExpression, DifferentialMethylation,\nDifferentialSplicing, DNAMethylation, Epigenetics,\nFunctionalGenomics, GeneExpression, GeneSetEnrichment,\nGenetics, Genetics, ImmunoOncology, MultipleComparison,\nNormalization, Pathways, Proteomics, QualityControl,\nRegression, RNASeq, SAGE, Sequencing, SingleCell,\nSystemsBiology, TimeCourse, Transcription, Transcriptomics",
  "NeedsCompilation": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-23 03:28:00 UTC",
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      "title": "Empirical analysis of digital gene expression data in R",
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        "edgeR-package",
        "edgeR"
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      "title": "Add a prior count",
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    {
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      "title": "Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter",
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        "camera.DGEList",
        "cameraPR.DGELRT"
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        "Reading data files"
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        "catchOarfish",
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        "cbind.DGEList",
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      "title": "Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries",
      "concept": [
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      "title": "Counts per Million or Reads per Kilobase per Million",
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        "Data exploration"
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        "cpmByGroup",
        "cpmByGroup.default",
        "cpmByGroup.DGEList",
        "cpmByGroup.SummarizedExperiment",
        "rpkm",
        "rpkm.default",
        "rpkm.DGEGLM",
        "rpkm.DGEList",
        "rpkm.DGELRT",
        "rpkm.MArrayLM",
        "rpkm.SummarizedExperiment",
        "rpkmByGroup",
        "rpkmByGroup.default",
        "rpkmByGroup.DGEList",
        "rpkmByGroup.SummarizedExperiment"
      ]
    },
    {
      "page": "cutWithMinN",
      "title": "Cut Numeric Vector Into Non-empty Intervals",
      "topics": [
        "cutWithMinN"
      ]
    },
    {
      "page": "decidetestsDGE",
      "title": "Multiple Testing Across Genes and Contrasts",
      "concept": [
        "Differential expression"
      ],
      "topics": [
        "decideTests.DGEExact",
        "decideTests.DGELRT"
      ]
    },
    {
      "page": "DGEExact-class",
      "title": "differential expression of Digital Gene Expression data - class",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "DGEExact-class",
        "show,DGEExact-method"
      ]
    },
    {
      "page": "DGEGLM-class",
      "title": "Digital Gene Expression Generalized Linear Model results - class",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "DGEGLM-class",
        "show,DGEGLM-method"
      ]
    },
    {
      "page": "DGEList",
      "title": "Create a DGEList object",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "DGEList",
        "DGEList.data.frame",
        "DGEList.default"
      ]
    },
    {
      "page": "DGEList-class",
      "title": "Digital Gene Expression data - class",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "DGEList-class"
      ]
    },
    {
      "page": "DGEListFromTximport",
      "title": "Create a DGEList Object From tximport or tximeta Output",
      "concept": [
        "edgeR classes",
        "Reading data files"
      ],
      "topics": [
        "DGEListFromTximeta",
        "DGEListFromTximport"
      ]
    },
    {
      "page": "DGELRT-class",
      "title": "Digital Gene Expression Likelihood Ratio Test data and results - class",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "DGELRT-class",
        "show,DGELRT-method"
      ]
    },
    {
      "page": "diffSplice",
      "title": "Differential Transcript or Exon Usage",
      "concept": [
        "Differential transcript usage",
        "Differential usage"
      ],
      "topics": [
        "diffSplice.DGEGLM"
      ]
    },
    {
      "page": "diffSpliceDGE",
      "title": "Test for Differential Exon Usage",
      "concept": [
        "Differential exon usage"
      ],
      "topics": [
        "diffSpliceDGE"
      ]
    },
    {
      "page": "dim",
      "title": "Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "dim.DGEExact",
        "dim.DGEGLM",
        "dim.DGEList",
        "dim.DGELRT",
        "dim.TopTags"
      ]
    },
    {
      "page": "dimnames",
      "title": "Retrieve the Dimension Names of a DGE Object",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "dimnames.DGEExact",
        "dimnames.DGEGLM",
        "dimnames.DGEList",
        "dimnames.DGELRT",
        "dimnames.TopTags",
        "dimnames<-.DGEExact",
        "dimnames<-.DGEGLM",
        "dimnames<-.DGEList",
        "dimnames<-.DGELRT"
      ]
    },
    {
      "page": "dispBinTrend",
      "title": "Estimate Dispersion Trend by Binning for NB GLMs",
      "topics": [
        "dispBinTrend"
      ]
    },
    {
      "page": "dispCoxReid",
      "title": "Estimate Common Dispersion for Negative Binomial GLMs",
      "topics": [
        "dispCoxReid",
        "dispDeviance",
        "dispPearson"
      ]
    },
    {
      "page": "dispCoxReidInterpolateTagwise",
      "title": "Estimate Genewise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "dispCoxReidInterpolateTagwise"
      ]
    },
    {
      "page": "dispCoxReidSplineTrend",
      "title": "Estimate Dispersion Trend for Negative Binomial GLMs",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "dispCoxReidPowerTrend",
        "dispCoxReidSplineTrend"
      ]
    },
    {
      "page": "dropEmptyLevels",
      "title": "Drop Levels of a Factor that Never Occur",
      "topics": [
        "dropEmptyLevels"
      ]
    },
    {
      "page": "edgeRUsersGuide",
      "title": "View edgeR User's Guide",
      "concept": [
        "Documentation"
      ],
      "topics": [
        "edgeRUsersGuide"
      ]
    },
    {
      "page": "equalizeLibSizes",
      "title": "Equalize Library Sizes by Quantile-to-Quantile Normalization",
      "concept": [
        "Normalization"
      ],
      "topics": [
        "equalizeLibSizes",
        "equalizeLibSizes.default",
        "equalizeLibSizes.DGEList"
      ]
    },
    {
      "page": "estimateCommonDisp",
      "title": "Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateCommonDisp",
        "estimateCommonDisp.default",
        "estimateCommonDisp.DGEList"
      ]
    },
    {
      "page": "estimateDisp",
      "title": "Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateDisp",
        "estimateDisp.default",
        "estimateDisp.DGEList",
        "estimateDisp.SummarizedExperiment"
      ]
    },
    {
      "page": "estimateExonGenewisedisp",
      "title": "Estimate Genewise Dispersions from Exon-Level Count Data",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateExonGenewiseDisp"
      ]
    },
    {
      "page": "estimateGLMCommonDisp",
      "title": "Estimate Common Dispersion for Negative Binomial GLMs",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateGLMCommonDisp",
        "estimateGLMCommonDisp.default",
        "estimateGLMCommonDisp.DGEList"
      ]
    },
    {
      "page": "estimateGLMRobustDisp",
      "title": "Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation Weights",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateGLMRobustDisp"
      ]
    },
    {
      "page": "estimateGLMTagwiseDisp",
      "title": "Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateGLMTagwiseDisp",
        "estimateGLMTagwiseDisp.default",
        "estimateGLMTagwiseDisp.DGEList"
      ]
    },
    {
      "page": "estimateGLMTrendedDisp",
      "title": "Estimate Trended Dispersion for Negative Binomial GLMs",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateGLMTrendedDisp",
        "estimateGLMTrendedDisp.default",
        "estimateGLMTrendedDisp.DGEList"
      ]
    },
    {
      "page": "estimateTagwiseDisp",
      "title": "Estimate Empirical Bayes Tagwise Dispersion Values",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateTagwiseDisp",
        "estimateTagwiseDisp.default",
        "estimateTagwiseDisp.DGEList"
      ]
    },
    {
      "page": "estimateTrendedDisp",
      "title": "Estimate Empirical Bayes Trended Dispersion Values",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "estimateTrendedDisp",
        "estimateTrendedDisp.default",
        "estimateTrendedDisp.DGEList"
      ]
    },
    {
      "page": "exactTest",
      "title": "Exact Tests for Differences between Two Groups of Negative-Binomial Counts",
      "concept": [
        "Differential expression"
      ],
      "topics": [
        "exactTest",
        "exactTestBetaApprox",
        "exactTestByDeviance",
        "exactTestBySmallP",
        "exactTestDoubleTail"
      ]
    },
    {
      "page": "expandAsMatrix",
      "title": "expandAsMatrix",
      "topics": [
        "expandAsMatrix"
      ]
    },
    {
      "page": "featureCounts2DGEList",
      "title": "Convert featureCounts object to a DGEList",
      "concept": [
        "edgeR classes",
        "differential transcript usage",
        "Differential usage"
      ],
      "topics": [
        "featureCounts2DGEList"
      ]
    },
    {
      "page": "filterByExpr",
      "title": "Filter Genes By Expression Level",
      "topics": [
        "filterByExpr",
        "filterByExpr.default",
        "filterByExpr.DGEList",
        "filterByExpr.SummarizedExperiment"
      ]
    },
    {
      "page": "getCounts",
      "title": "Extract Components of a DGEList Object",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "getCounts",
        "getDispersion",
        "getOffset"
      ]
    },
    {
      "page": "effectiveLibSizes",
      "title": "Effective Library Sizes",
      "concept": [
        "Normalization"
      ],
      "topics": [
        "getNormLibSizes",
        "getNormLibSizes.default",
        "getNormLibSizes.DGEGLM",
        "getNormLibSizes.DGEList",
        "getNormLibSizes.DGELRT"
      ]
    },
    {
      "page": "getPriorN",
      "title": "Get a Recommended Value for Prior N from DGEList Object",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "getPriorN"
      ]
    },
    {
      "page": "gini",
      "title": "Gini dispersion index",
      "concept": [
        "Data exploration"
      ],
      "topics": [
        "gini"
      ]
    },
    {
      "page": "glmfit",
      "title": "Genewise Negative Binomial Generalized Linear Models",
      "concept": [
        "Model fit",
        "Differential expression"
      ],
      "topics": [
        "glmFit",
        "glmFit.default",
        "glmFit.DGEList",
        "glmFit.SummarizedExperiment"
      ]
    },
    {
      "page": "glmLRT",
      "title": "Genewise Likelihood Ratio Tests",
      "concept": [
        "Model fit",
        "Differential expression"
      ],
      "topics": [
        "glmLRT"
      ]
    },
    {
      "page": "glmQLFit",
      "title": "Genewise Negative Binomial Generalized Linear Models with Quasi-Dispersion Estimation",
      "concept": [
        "Model fit",
        "Dispersion estimation",
        "Differential expression"
      ],
      "topics": [
        "glmQLFit",
        "glmQLFit.default",
        "glmQLFit.DGEList",
        "glmQLFit.SummarizedExperiment"
      ]
    },
    {
      "page": "glmQLFTest",
      "title": "Quasi-Likelihood F-Tests",
      "concept": [
        "Model fit",
        "Differential expression"
      ],
      "topics": [
        "glmQLFTest"
      ]
    },
    {
      "page": "glmTreat",
      "title": "Test for Differential Expression Relative to a Threshold",
      "topics": [
        "glmTreat"
      ]
    },
    {
      "page": "goana",
      "title": "Gene Ontology or KEGG Analysis of Differentially Expressed Genes",
      "concept": [
        "Gene set testing"
      ],
      "topics": [
        "goana.DGEExact",
        "goana.DGELRT",
        "kegga.DGEExact",
        "kegga.DGELRT"
      ]
    },
    {
      "page": "gof",
      "title": "Goodness of Fit Tests for Multiple GLM Fits",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "gof"
      ]
    },
    {
      "page": "goodTuring",
      "title": "Good-Turing Frequency Estimation",
      "concept": [
        "Normalization"
      ],
      "topics": [
        "goodTuring",
        "goodTuringPlot",
        "goodTuringProportions"
      ]
    },
    {
      "page": "head",
      "title": "Return the First to Last Part of a Data Object",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "head.DGEExact",
        "head.DGEGLM",
        "head.DGEList",
        "head.DGELRT",
        "head.TopTags",
        "tail.DGEExact",
        "tail.DGEGLM",
        "tail.DGEList",
        "tail.DGELRT",
        "tail.TopTags"
      ]
    },
    {
      "page": "loessByCol",
      "title": "Locally Weighted Mean By Column",
      "topics": [
        "locfitByCol",
        "loessByCol"
      ]
    },
    {
      "page": "makeCompressedMatrix",
      "title": "Make a CompressedMatrix",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "as.matrix.CompressedMatrix",
        "cbind.CompressedMatrix",
        "CompressedMatrix",
        "CompressedMatrix-class",
        "dim.CompressedMatrix",
        "length.CompressedMatrix",
        "makeCompressedMatrix",
        "Ops.CompressedMatrix",
        "rbind.CompressedMatrix",
        "[.CompressedMatrix",
        "[<-.CompressedMatrix"
      ]
    },
    {
      "page": "maPlot",
      "title": "Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "maPlot"
      ]
    },
    {
      "page": "maximizeInterpolant",
      "title": "Maximize a function given a table of values by spline interpolation.",
      "topics": [
        "maximizeInterpolant"
      ]
    },
    {
      "page": "maximizeQuadratic",
      "title": "Maximize a function given a table of values by quadratic interpolation.",
      "topics": [
        "maximizeQuadratic"
      ]
    },
    {
      "page": "meanvar",
      "title": "Explore the Mean-Variance Relationship for DGE Data",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "binMeanVar",
        "plotMeanVar"
      ]
    },
    {
      "page": "mglm",
      "title": "Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "designAsFactor",
        "mglm",
        "mglmLevenberg",
        "mglmOneGroup",
        "mglmOneWay"
      ]
    },
    {
      "page": "modelMatrixMeth",
      "title": "Construct Design Matrix for edgeR Analysis of Methylation Count Data",
      "concept": [
        "Differential methylation"
      ],
      "topics": [
        "modelMatrixMeth"
      ]
    },
    {
      "page": "movingAverageByCol",
      "title": "Moving Average Smoother of Matrix Columns",
      "topics": [
        "movingAverageByCol"
      ]
    },
    {
      "page": "nbinomDeviance",
      "title": "Negative Binomial Deviance",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "nbinomDeviance"
      ]
    },
    {
      "page": "nbinomUnitDeviance",
      "title": "Negative Binomial Unit Deviance",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "nbinomUnitDeviance"
      ]
    },
    {
      "page": "nearestReftoX",
      "title": "Find Nearest Element of Reference for each Element of X",
      "topics": [
        "nearestReftoX"
      ]
    },
    {
      "page": "nearestTSS",
      "title": "Find Nearest Transcriptional Start Site",
      "topics": [
        "nearestTSS"
      ]
    },
    {
      "page": "normalizeBetweenArraysDGEList",
      "title": "Apply Microarray Normalization to DGEList",
      "topics": [
        "normalizeBetweenArrays.DGEList"
      ]
    },
    {
      "page": "normalizeChIPtoInput",
      "title": "Normalize ChIP-Seq Read Counts to Input and Test for Enrichment",
      "concept": [
        "Normalization"
      ],
      "topics": [
        "calcNormOffsetsforChIP",
        "normalizeChIPtoInput"
      ]
    },
    {
      "page": "calcNormFactors",
      "title": "Normalize Library Sizes",
      "concept": [
        "Normalization"
      ],
      "topics": [
        "calcNormFactors",
        "calcNormFactors.default",
        "calcNormFactors.DGEList",
        "calcNormFactors.SummarizedExperiment",
        "normLibSizes",
        "normLibSizes.default",
        "normLibSizes.DGEList",
        "normLibSizes.SummarizedExperiment"
      ]
    },
    {
      "page": "plotBCV",
      "title": "Plot Biological Coefficient of Variation",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "plotBCV"
      ]
    },
    {
      "page": "plotExonUsage",
      "title": "Create a Plot of Exon Usage from Exon-Level Count Data",
      "concept": [
        "Differential exon usage"
      ],
      "topics": [
        "plotExonUsage"
      ]
    },
    {
      "page": "plotMD",
      "title": "Mean-Difference Plot of Count Data",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "plotMD.DGEExact",
        "plotMD.DGEGLM",
        "plotMD.DGEList",
        "plotMD.DGELRT",
        "plotMD.SummarizedExperiment"
      ]
    },
    {
      "page": "plotMDS.DGEList",
      "title": "Multidimensional scaling plot of distances between digital gene expression profiles",
      "concept": [
        "Data exploration"
      ],
      "topics": [
        "plotMDS.DGEList",
        "plotMDS.SummarizedExperiment"
      ]
    },
    {
      "page": "dglmStdResid",
      "title": "Plot Mean-Variance Relationship in DGE Data Using Standardized Residuals",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "plotMeanVar2"
      ]
    },
    {
      "page": "plotQLDisp",
      "title": "Plot the quasi-dispersion",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "plotQLDisp"
      ]
    },
    {
      "page": "plotSmear",
      "title": "Smear plot",
      "concept": [
        "Data exploration",
        "Model fit"
      ],
      "topics": [
        "plotSmear"
      ]
    },
    {
      "page": "plotSpliceDGE",
      "title": "Differential splicing plot",
      "concept": [
        "Differential exon usage"
      ],
      "topics": [
        "plotSpliceDGE"
      ]
    },
    {
      "page": "predFC",
      "title": "Predictive log-fold changes",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "predFC",
        "predFC.default",
        "predFC.DGEList",
        "predFC.SummarizedExperiment"
      ]
    },
    {
      "page": "processAmplicons",
      "title": "Process FASTQ files from pooled genetic sequencing screens",
      "topics": [
        "processAmplicons"
      ]
    },
    {
      "page": "q2qnbinom",
      "title": "Quantile to Quantile Mapping between Negative-Binomial Distributions",
      "concept": [
        "Normalization"
      ],
      "topics": [
        "q2qnbinom",
        "q2qpois"
      ]
    },
    {
      "page": "read10X",
      "title": "Read 10X Genomics Files",
      "concept": [
        "Reading data files"
      ],
      "topics": [
        "read10X"
      ]
    },
    {
      "page": "readBismark2DGE",
      "title": "Read Bismark Coverage Files",
      "concept": [
        "Reading data files",
        "Differential methylation"
      ],
      "topics": [
        "readBismark2DGE"
      ]
    },
    {
      "page": "readDGE",
      "title": "Read and Merge a Set of Files Containing Count Data",
      "concept": [
        "Reading data files"
      ],
      "topics": [
        "readDGE"
      ]
    },
    {
      "page": "roast.DGEGLM",
      "title": "Self-contained Gene Set Tests for Digital Gene Expression Data",
      "concept": [
        "Gene set testing"
      ],
      "topics": [
        "fry.DGEGLM",
        "mroast.DGEGLM",
        "roast.DGEGLM"
      ]
    },
    {
      "page": "roast.DGEList",
      "title": "Self-contained Gene Set Tests for Digital Gene Expression Data",
      "concept": [
        "Gene set testing"
      ],
      "topics": [
        "fry.DGEList",
        "mroast.DGEList",
        "roast.DGEList"
      ]
    },
    {
      "page": "romer.DGEGLM",
      "title": "Rotation Gene Set Enrichment for Digital Gene Expression Data",
      "concept": [
        "Gene set testing"
      ],
      "topics": [
        "romer.DGEGLM"
      ]
    },
    {
      "page": "romer.DGEList",
      "title": "Rotation Gene Set Enrichment for Digital Gene Expression Data",
      "concept": [
        "Gene set testing"
      ],
      "topics": [
        "romer.DGEList"
      ]
    },
    {
      "page": "rowsum",
      "title": "Sum Over Groups of Genes",
      "topics": [
        "rowsum.DGEList",
        "rowsum.SummarizedExperiment"
      ]
    },
    {
      "page": "sampleWeights",
      "title": "Empirical Sample Quality Weights",
      "topics": [
        "sampleWeights"
      ]
    },
    {
      "page": "scaleOffset",
      "title": "Scale offsets",
      "concept": [
        "Normalization"
      ],
      "topics": [
        "scaleOffset",
        "scaleOffset.default",
        "scaleOffset.DGEList"
      ]
    },
    {
      "page": "SE2DGEList",
      "title": "SummarizedExperiment to DGEList",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "SE2DGEList"
      ]
    },
    {
      "page": "Seurat2PB",
      "title": "Seurat or SeuratObject class object to pseudo-bulk DGEList",
      "concept": [
        "edgeR classes"
      ],
      "topics": [
        "Seurat2PB"
      ]
    },
    {
      "page": "spliceVariants",
      "title": "Identify Genes with Splice Variants (Classic Pipeline)",
      "concept": [
        "Differential exon usage"
      ],
      "topics": [
        "spliceVariants"
      ]
    },
    {
      "page": "splitIntoGroups",
      "title": "Split the Counts or Pseudocounts from a DGEList Object According To Group",
      "topics": [
        "splitIntoGroups",
        "splitIntoGroups.default",
        "splitIntoGroups.DGEList",
        "splitIntoGroupsPseudo"
      ]
    },
    {
      "page": "subsetting",
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