{
  "_id": "6ae66ef32e87f76f20acc04d",
  "Package": "edgeR",
  "Version": "4.99.11",
  "Date": "2026-10-31",
  "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>",
  "License": "GPL (>=2)",
  "VignetteBuilder": "knitr",
  "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": "2026-10-31 21:11:33 UTC",
  "RemoteUrl": "https://github.com/bioc/edgeR",
  "RemoteRef": "HEAD",
  "RemoteSha": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
  "Packaged": {
    "Date": "2026-10-31 22:26:08 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "edgeR_4.99.11.tar.gz",
  "_fileid": "https://r2.ropensci.org/3729e7c06c9147d09023c40f365f35b7ed3730bb0ddf894e8a724f8d22321d09",
  "_filesize": 3659996,
  "_sha256": "3729e7c06c9147d09023c40f365f35b7ed3730bb0ddf894e8a724f8d22321d09",
  "_expires": "2027-02-08T22:42:57.000Z",
  "_created": "2026-10-31T22:26:08.000Z",
  "_published": "2026-10-31T22:42:58.859Z",
  "_upstream": "https://github.com/bioc/edgeR",
  "_status": "success",
  "_maintainer": {
    "name": "Yunshun Chen",
    "email": "yuchen@wehi.edu.au",
    "login": "yunshun",
    "description": "",
    "uuid": 22924100
  },
  "_jobs": [
    {
      "job": 124676044124,
      "time": 246,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "13060067854"
    },
    {
      "job": 124676044180,
      "time": 165,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13059967871"
    },
    {
      "job": 124676044183,
      "time": 258,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13059733562"
    },
    {
      "job": 124676044248,
      "time": 162,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13060596517"
    },
    {
      "job": 124676044195,
      "time": 220,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "13060561676"
    },
    {
      "job": 124676044334,
      "time": 162,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13060378730"
    },
    {
      "job": 124676044229,
      "time": 235,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13060143453"
    },
    {
      "job": 124676044264,
      "time": 197,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13060627670"
    },
    {
      "job": 124676044209,
      "time": 346,
      "config": "macos-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13059704863"
    },
    {
      "job": 124675035225,
      "time": 267,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13060296059"
    },
    {
      "job": 124676044196,
      "time": 117,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13060651350"
    },
    {
      "job": 124676044297,
      "time": 274,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13060306450"
    },
    {
      "job": 124676044301,
      "time": 220,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13060347184"
    },
    {
      "job": 124676044424,
      "time": 186,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13059921878"
    },
    {
      "job": 124676044324,
      "time": 268,
      "config": "windows-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13060052943"
    },
    {
      "job": 124676044283,
      "time": 182,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13060311306"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 18
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548",
  "_commit": {
    "id": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
    "author": "Gordon Smyth <smyth@wehi.edu.au>",
    "committer": "Gordon Smyth <smyth@wehi.edu.au>",
    "message": "edgeR 3.99.11 (continued)\n- Add catchOarfishGene.R and locfit_lite.c\n",
    "time": 1793481093
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "limma",
      "version": ">= 3.63.6",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "nanoparquet",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rhdf5",
      "role": "Suggests"
    },
    {
      "package": "SeuratObject",
      "role": "Suggests"
    },
    {
      "package": "splines",
      "role": "Suggests"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "Biobase",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "S4Vectors",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 319,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2025-52",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 1
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-15",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 3
    },
    {
      "week": "2026-17",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-21",
      "n": 1
    },
    {
      "week": "2026-26",
      "n": 3
    },
    {
      "week": "2026-32",
      "n": 4
    },
    {
      "week": "2026-34",
      "n": 1
    },
    {
      "week": "2026-35",
      "n": 1
    },
    {
      "week": "2026-36",
      "n": 5
    },
    {
      "week": "2026-37",
      "n": 4
    },
    {
      "week": "2026-42",
      "n": 6
    },
    {
      "week": "2026-44",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "4.99.10",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "4.10.7",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "alternativesplicing",
    "batcheffect",
    "bayesian",
    "biomedicalinformatics",
    "cellbiology",
    "chipseq",
    "clustering",
    "coverage",
    "differentialexpression",
    "differentialmethylation",
    "differentialsplicing",
    "dnamethylation",
    "epigenetics",
    "functionalgenomics",
    "geneexpression",
    "genesetenrichment",
    "genetics",
    "immunooncology",
    "multiplecomparison",
    "normalization",
    "pathways",
    "proteomics",
    "qualitycontrol",
    "regression",
    "rnaseq",
    "sage",
    "sequencing",
    "singlecell",
    "systemsbiology",
    "timecourse",
    "transcription",
    "transcriptomics",
    "openblas",
    "openmp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 481,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 57272,
    "source": "https://www.bioconductor.org/packages/stats/bioc/edgeR"
  },
  "_mentions": 6568,
  "_searchresults": 31200,
  "_abi": {
    "exports": [
      {
        "key": "edgeR::DGEBIN",
        "hash": "c589913425d2083f"
      },
      {
        "key": "edgeR::DGEExact",
        "hash": "1b287634eaa8480e"
      },
      {
        "key": "edgeR::DGEGLM",
        "hash": "20f042ed7819b270"
      },
      {
        "key": "edgeR::DGELRT",
        "hash": "0e963fca9176edbc"
      },
      {
        "key": "edgeR::DGEList",
        "hash": "f36007ff867bfa20"
      },
      {
        "key": "edgeR::PCList",
        "hash": "27dcabdd71b933b4"
      },
      {
        "key": "edgeR::TopTags",
        "hash": "7ac46986bd2e805e"
      }
    ],
    "imports": [
      {
        "key": "limma::LargeDataObject",
        "hash": "75f2d5f9c397ea75"
      }
    ]
  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/edgeR.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "[.CompressedMatrix",
    "[.DGEBIN",
    "[.DGEExact",
    "[.DGEGLM",
    "[.DGEList",
    "[.DGELRT",
    "[.PCList",
    "[.TopTags",
    "[<-.CompressedMatrix",
    "addPriorCount",
    "adjustedProfileLik",
    "as.data.frame.DGEBIN",
    "as.data.frame.DGEExact",
    "as.data.frame.DGEGLM",
    "as.data.frame.DGEList",
    "as.data.frame.DGELRT",
    "as.data.frame.PCList",
    "as.data.frame.TopTags",
    "as.matrix.CompressedMatrix",
    "as.matrix.DGEBIN",
    "as.matrix.DGEGLM",
    "as.matrix.DGEList",
    "aveLogCPM",
    "aveLogCPM.default",
    "aveLogCPM.DGEGLM",
    "aveLogCPM.DGEList",
    "aveLogCPM.PCList",
    "aveLogCPM.SummarizedExperiment",
    "binFit",
    "binFit.default",
    "binFit.PCList",
    "binMeanVar",
    "binomTest",
    "binQLFit",
    "binQLFit.default",
    "binQLFit.PCList",
    "binQLFTest",
    "calcNormFactors",
    "calcNormFactors.default",
    "calcNormFactors.DGEList",
    "calcNormFactors.SummarizedExperiment",
    "calcNormOffsetsforChIP",
    "camera.DGEGLM",
    "camera.DGEList",
    "cameraPR.DGELRT",
    "catchKallisto",
    "catchKallistoGene",
    "catchOarfish",
    "catchOarfishGene",
    "catchRSEM",
    "catchSalmon",
    "catchSalmonGene",
    "cbind.CompressedMatrix",
    "cbind.DGEList",
    "collapseGencodeTx2Gene",
    "commonCondLogLikDerDelta",
    "condLogLikDerDelta",
    "condLogLikDerSize",
    "cpm",
    "cpm.default",
    "cpm.DGEGLM",
    "cpm.DGEList",
    "cpm.DGELRT",
    "cpm.MArrayLM",
    "cpm.SummarizedExperiment",
    "cpmByGroup",
    "cpmByGroup.default",
    "cpmByGroup.DGEList",
    "cpmByGroup.SummarizedExperiment",
    "cutWithMinN",
    "decideTests.DGEExact",
    "decideTests.DGELRT",
    "designAsFactor",
    "DGEList",
    "DGEList.data.frame",
    "DGEList.default",
    "DGEListFromTximeta",
    "DGEListFromTximport",
    "diffSplice.DGEGLM",
    "diffSpliceDGE",
    "dim.CompressedMatrix",
    "dim.DGEBIN",
    "dim.DGEExact",
    "dim.DGEGLM",
    "dim.DGEList",
    "dim.DGELRT",
    "dim.PCList",
    "dim.TopTags",
    "dimnames.DGEBIN",
    "dimnames.DGEExact",
    "dimnames.DGEGLM",
    "dimnames.DGEList",
    "dimnames.DGELRT",
    "dimnames.PCList",
    "dimnames.TopTags",
    "dimnames<-.DGEBIN",
    "dimnames<-.DGEExact",
    "dimnames<-.DGEGLM",
    "dimnames<-.DGEList",
    "dimnames<-.DGELRT",
    "dimnames<-.PCList",
    "dispBinTrend",
    "dispCoxReid",
    "dispCoxReidInterpolateTagwise",
    "dispCoxReidPowerTrend",
    "dispCoxReidSplineTrend",
    "dispDeviance",
    "dispPearson",
    "dropEmptyLevels",
    "edgeRUsersGuide",
    "equalizeLibSizes",
    "equalizeLibSizes.default",
    "equalizeLibSizes.DGEList",
    "estimateCommonDisp",
    "estimateCommonDisp.default",
    "estimateCommonDisp.DGEList",
    "estimateDisp",
    "estimateDisp.default",
    "estimateDisp.DGEList",
    "estimateDisp.SummarizedExperiment",
    "estimateExonGenewiseDisp",
    "estimateGLMCommonDisp",
    "estimateGLMCommonDisp.default",
    "estimateGLMCommonDisp.DGEList",
    "estimateGLMRobustDisp",
    "estimateGLMTagwiseDisp",
    "estimateGLMTagwiseDisp.default",
    "estimateGLMTagwiseDisp.DGEList",
    "estimateGLMTrendedDisp",
    "estimateGLMTrendedDisp.default",
    "estimateGLMTrendedDisp.DGEList",
    "estimateTagwiseDisp",
    "estimateTagwiseDisp.default",
    "estimateTagwiseDisp.DGEList",
    "estimateTrendedDisp",
    "estimateTrendedDisp.default",
    "estimateTrendedDisp.DGEList",
    "estimateTxExpr",
    "exactTest",
    "exactTestBetaApprox",
    "exactTestByDeviance",
    "exactTestBySmallP",
    "exactTestDoubleTail",
    "expandAsMatrix",
    "featureCounts2DGEList",
    "filterByExpr",
    "filterByExpr.default",
    "filterByExpr.DGEList",
    "filterByExpr.SummarizedExperiment",
    "fry.DGEGLM",
    "fry.DGEList",
    "getCounts",
    "getDispersion",
    "getNormLibSizes",
    "getNormLibSizes.default",
    "getNormLibSizes.DGEGLM",
    "getNormLibSizes.DGEList",
    "getNormLibSizes.DGELRT",
    "getOffset",
    "getPriorN",
    "gini",
    "glmFit",
    "glmFit.default",
    "glmFit.DGEList",
    "glmFit.SummarizedExperiment",
    "glmLRT",
    "glmQLFit",
    "glmQLFit.default",
    "glmQLFit.DGEList",
    "glmQLFit.SummarizedExperiment",
    "glmQLFTest",
    "glmTreat",
    "goana.DGEExact",
    "goana.DGELRT",
    "gof",
    "goodTuring",
    "goodTuringPlot",
    "goodTuringProportions",
    "head.DGEBIN",
    "head.DGEExact",
    "head.DGEGLM",
    "head.DGEList",
    "head.DGELRT",
    "head.PCList",
    "head.TopTags",
    "kegga.DGEExact",
    "kegga.DGELRT",
    "length.CompressedMatrix",
    "locfitByCol",
    "loessByCol",
    "makeCompressedMatrix",
    "maPlot",
    "maximizeInterpolant",
    "maximizeQuadratic",
    "mbinIWLS",
    "mbinOneWay",
    "mglmLevenberg",
    "mglmOneGroup",
    "mglmOneWay",
    "modelMatrixMeth",
    "movingAverageByCol",
    "mroast.DGEGLM",
    "mroast.DGEList",
    "nbinomDeviance",
    "nbinomUnitDeviance",
    "nearestReftoX",
    "nearestTSS",
    "normalizeBetweenArrays.DGEList",
    "normalizeChIPtoInput",
    "normLibSizes",
    "normLibSizes.default",
    "normLibSizes.DGEList",
    "normLibSizes.SummarizedExperiment",
    "Ops.CompressedMatrix",
    "PCList",
    "plotBCV",
    "plotExonUsage",
    "plotMD.DGEBIN",
    "plotMD.DGEExact",
    "plotMD.DGEGLM",
    "plotMD.DGEList",
    "plotMD.DGELRT",
    "plotMD.SummarizedExperiment",
    "plotMDS.DGEList",
    "plotMDS.PCList",
    "plotMDS.SummarizedExperiment",
    "plotMeanVar",
    "plotMeanVar2",
    "plotQLDisp",
    "plotSmear",
    "plotSpliceDGE",
    "predFC",
    "predFC.default",
    "predFC.DGEList",
    "predFC.SummarizedExperiment",
    "processAmplicons",
    "q2qnbinom",
    "q2qpois",
    "rbind.CompressedMatrix",
    "rbind.DGEList",
    "read10X",
    "readBismark2DGE",
    "readBismark2PC",
    "readDGE",
    "roast.DGEGLM",
    "roast.DGEList",
    "romer.DGEGLM",
    "romer.DGEList",
    "rowsum.DGEList",
    "rowsum.PCList",
    "rowsum.SummarizedExperiment",
    "rpkm",
    "rpkm.default",
    "rpkm.DGEGLM",
    "rpkm.DGEList",
    "rpkm.DGELRT",
    "rpkm.MArrayLM",
    "rpkm.SummarizedExperiment",
    "rpkmByGroup",
    "rpkmByGroup.default",
    "rpkmByGroup.DGEList",
    "rpkmByGroup.SummarizedExperiment",
    "sampleWeights",
    "scaleOffset",
    "scaleOffset.default",
    "scaleOffset.DGEList",
    "SE2DGEList",
    "Seurat2PB",
    "show",
    "spliceVariants",
    "splitGencodeTxNames",
    "splitIntoGroups",
    "splitIntoGroups.default",
    "splitIntoGroups.DGEList",
    "splitIntoGroupsPseudo",
    "sumTechReps",
    "sumTechReps.default",
    "sumTechReps.DGEList",
    "sumTechReps.SummarizedExperiment",
    "systematicSubset",
    "tail.DGEBIN",
    "tail.DGEExact",
    "tail.DGEGLM",
    "tail.DGEList",
    "tail.DGELRT",
    "tail.PCList",
    "tail.TopTags",
    "thinCounts",
    "topSpliceDGE",
    "topTags",
    "tpm",
    "tpmProp",
    "validDGEList",
    "weightedCondLogLikDerDelta",
    "WLEB",
    "zscoreNBinom"
  ],
  "_help": [
    {
      "page": "edgeR-package",
      "title": "Empirical Analysis of Digital Gene Expression Data in R",
      "concept": [
        "Documentation"
      ],
      "topics": [
        "edgeR-package",
        "edgeR"
      ]
    },
    {
      "page": "addPriorCount",
      "title": "Add a Prior Count",
      "topics": [
        "addPriorCount"
      ]
    },
    {
      "page": "adjustedProfileLik",
      "title": "Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "adjustedProfileLik"
      ]
    },
    {
      "page": "asdataframe",
      "title": "Collapse TopTags or Other edgeR Object to a Data Frame",
      "concept": [
        "Classes"
      ],
      "topics": [
        "as.data.frame.DGEBIN",
        "as.data.frame.DGEExact",
        "as.data.frame.DGEGLM",
        "as.data.frame.DGEList",
        "as.data.frame.DGELRT",
        "as.data.frame.PCList",
        "as.data.frame.TopTags"
      ]
    },
    {
      "page": "asmatrix",
      "title": "Collapse a DGEList or DGEGLM Object to a Matrix",
      "concept": [
        "Classes"
      ],
      "topics": [
        "as.matrix.DGEBIN",
        "as.matrix.DGEGLM",
        "as.matrix.DGEList"
      ]
    },
    {
      "page": "aveLogCPM",
      "title": "Average Log Counts per Million",
      "topics": [
        "aveLogCPM",
        "aveLogCPM.default",
        "aveLogCPM.DGEGLM",
        "aveLogCPM.DGEList",
        "aveLogCPM.PCList",
        "aveLogCPM.SummarizedExperiment"
      ]
    },
    {
      "page": "binfit",
      "title": "Genewise Binomial Generalized Linear Models",
      "concept": [
        "Model fit",
        "Differential methylation"
      ],
      "topics": [
        "binFit",
        "binFit.default",
        "binFit.PCList"
      ]
    },
    {
      "page": "binomTest",
      "title": "Exact Binomial Tests for Comparing Two Digital Libraries",
      "concept": [
        "Differential expression"
      ],
      "topics": [
        "binomTest"
      ]
    },
    {
      "page": "binQLFit",
      "title": "Quasi-Likelihood Binomial Generalized Linear Models",
      "concept": [
        "Model fit",
        "Differential methylation"
      ],
      "topics": [
        "binQLFit",
        "binQLFit.default",
        "binQLFit.PCList"
      ]
    },
    {
      "page": "binQLFTest",
      "title": "Quasi-Likelihood F-Tests for Binomial Models",
      "concept": [
        "Model fit",
        "Differential methylation"
      ],
      "topics": [
        "binQLFTest"
      ]
    },
    {
      "page": "camera",
      "title": "Competitive Gene Set Tests for Digital Gene Expression Data",
      "topics": [
        "camera.DGEGLM",
        "camera.DGEList",
        "cameraPR.DGELRT"
      ]
    },
    {
      "page": "catchSalmon",
      "title": "Process kallisto, Salmon, Oarfish, or RSEM Transcript Output",
      "concept": [
        "Transcript expression",
        "Reading data files"
      ],
      "topics": [
        "catchKallisto",
        "catchOarfish",
        "catchRSEM",
        "catchSalmon"
      ]
    },
    {
      "page": "catchSalmonGene",
      "title": "Process Kallisto or Salmon Output to Produce Gene Counts",
      "concept": [
        "Transcript expression",
        "Reading data files"
      ],
      "topics": [
        "catchKallistoGene",
        "catchOarfishGene",
        "catchSalmonGene"
      ]
    },
    {
      "page": "cbind",
      "title": "Combine DGEList Objects",
      "concept": [
        "Classes"
      ],
      "topics": [
        "cbind",
        "cbind.DGEList",
        "rbind.DGEList"
      ]
    },
    {
      "page": "commonCondLogLikDerDelta",
      "title": "Conditional Log-Likelihoods in Terms of Delta",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "commonCondLogLikDerDelta"
      ]
    },
    {
      "page": "condLogLikDerSize",
      "title": "Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "condLogLikDerDelta",
        "condLogLikDerSize"
      ]
    },
    {
      "page": "cpm",
      "title": "Counts per Million or Reads per Kilobase per Million",
      "concept": [
        "Data exploration"
      ],
      "topics": [
        "cpm",
        "cpm.default",
        "cpm.DGEGLM",
        "cpm.DGEList",
        "cpm.DGELRT",
        "cpm.MArrayLM",
        "cpm.SummarizedExperiment",
        "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": "DGEBIN-class",
      "title": "Digital Gene Expression Binomial Model Results - Class",
      "concept": [
        "Classes"
      ],
      "topics": [
        "DGEBIN-class",
        "show,DGEBIN-method"
      ]
    },
    {
      "page": "DGEExact-class",
      "title": "Differential Expression of Digital Gene Expression Data - Class",
      "concept": [
        "Classes"
      ],
      "topics": [
        "DGEExact-class",
        "show,DGEExact-method"
      ]
    },
    {
      "page": "DGEGLM-class",
      "title": "Digital Gene Expression Generalized Linear Model Results - Class",
      "concept": [
        "Classes"
      ],
      "topics": [
        "DGEGLM-class",
        "show,DGEGLM-method"
      ]
    },
    {
      "page": "DGEList",
      "title": "Create a DGEList Object",
      "concept": [
        "Classes"
      ],
      "topics": [
        "DGEList",
        "DGEList.data.frame",
        "DGEList.default"
      ]
    },
    {
      "page": "DGEList-class",
      "title": "Digital Gene Expression Data - Class",
      "concept": [
        "Classes"
      ],
      "topics": [
        "DGEList-class"
      ]
    },
    {
      "page": "DGEListFromTximport",
      "title": "Create a DGEList Object from tximport or tximeta Output",
      "concept": [
        "Classes",
        "Reading data files"
      ],
      "topics": [
        "DGEListFromTximeta",
        "DGEListFromTximport"
      ]
    },
    {
      "page": "DGELRT-class",
      "title": "Digital Gene Expression Likelihood Ratio Test Data and Results - Class",
      "concept": [
        "Classes"
      ],
      "topics": [
        "DGELRT-class",
        "show,DGELRT-method"
      ]
    },
    {
      "page": "diffSplice",
      "title": "Differential Transcript or Exon Usage",
      "concept": [
        "Differential usage"
      ],
      "topics": [
        "diffSplice.DGEGLM"
      ]
    },
    {
      "page": "diffSpliceDGE",
      "title": "Test for Differential Exon Usage",
      "concept": [
        "Differential usage"
      ],
      "topics": [
        "diffSpliceDGE"
      ]
    },
    {
      "page": "dim",
      "title": "Retrieve the Dimensions of a DGEList, PCList, DGEExact, DGEGLM, DGELRT or TopTags Object",
      "concept": [
        "Classes"
      ],
      "topics": [
        "dim.DGEBIN",
        "dim.DGEExact",
        "dim.DGEGLM",
        "dim.DGEList",
        "dim.DGELRT",
        "dim.PCList",
        "dim.TopTags"
      ]
    },
    {
      "page": "dimnames",
      "title": "Retrieve the Dimension Names of a DGE Object",
      "concept": [
        "Classes"
      ],
      "topics": [
        "dimnames.DGEBIN",
        "dimnames.DGEExact",
        "dimnames.DGEGLM",
        "dimnames.DGEList",
        "dimnames.DGELRT",
        "dimnames.PCList",
        "dimnames.TopTags",
        "dimnames<-.DGEBIN",
        "dimnames<-.DGEExact",
        "dimnames<-.DGEGLM",
        "dimnames<-.DGEList",
        "dimnames<-.DGELRT",
        "dimnames<-.PCList"
      ]
    },
    {
      "page": "dispBinTrend",
      "title": "Estimate Dispersion Trend by Binning for NB GLMs",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "dispBinTrend"
      ]
    },
    {
      "page": "dispCoxReid",
      "title": "Estimate Common Dispersion for Negative Binomial GLMs",
      "concept": [
        "Dispersion estimation"
      ],
      "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": "estimateTxExpr",
      "title": "Estimate Transcript Expression Levels from Equivalence Class Counts",
      "concept": [
        "Transcript expression"
      ],
      "topics": [
        "estimateTxExpr"
      ]
    },
    {
      "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": "Expand to a Matrix",
      "topics": [
        "expandAsMatrix"
      ]
    },
    {
      "page": "featureCounts2DGEList",
      "title": "Convert featureCounts Object to a DGEList",
      "concept": [
        "Classes",
        "Differential usage"
      ],
      "topics": [
        "featureCounts2DGEList"
      ]
    },
    {
      "page": "filterByExpr",
      "title": "Filter Genes by Expression Level",
      "concept": [
        "Preprocessing"
      ],
      "topics": [
        "filterByExpr",
        "filterByExpr.default",
        "filterByExpr.DGEList",
        "filterByExpr.SummarizedExperiment"
      ]
    },
    {
      "page": "getCounts",
      "title": "Extract Components of a DGEList Object",
      "concept": [
        "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": [
        "Classes"
      ],
      "topics": [
        "head.DGEBIN",
        "head.DGEExact",
        "head.DGEGLM",
        "head.DGEList",
        "head.DGELRT",
        "head.PCList",
        "head.TopTags",
        "tail.DGEBIN",
        "tail.DGEExact",
        "tail.DGEGLM",
        "tail.DGEList",
        "tail.DGELRT",
        "tail.PCList",
        "tail.TopTags"
      ]
    },
    {
      "page": "loessByCol",
      "title": "Locally Weighted Mean by Column",
      "topics": [
        "locfitByCol",
        "loessByCol"
      ]
    },
    {
      "page": "makeCompressedMatrix",
      "title": "Make a CompressedMatrix",
      "concept": [
        "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": "mBin",
      "title": "Fit Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "mbin",
        "mbinIWLS",
        "mbinOneWay"
      ]
    },
    {
      "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": "PCList",
      "title": "Create a PCList Object",
      "concept": [
        "Classes"
      ],
      "topics": [
        "PCList"
      ]
    },
    {
      "page": "PCList-class",
      "title": "Paired Counts Data Object - Class",
      "concept": [
        "Classes"
      ],
      "topics": [
        "PCList-class"
      ]
    },
    {
      "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 usage"
      ],
      "topics": [
        "plotExonUsage"
      ]
    },
    {
      "page": "plotMD",
      "title": "Mean-Difference Plot of Count Data",
      "concept": [
        "Model fit"
      ],
      "topics": [
        "plotMD.DGEBIN",
        "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": "plotMDS.PCList",
      "title": "Multidimensional Scaling Plot of Distances between M-values from the Paired Count Data",
      "concept": [
        "Data exploration"
      ],
      "topics": [
        "plotMDS.PCList"
      ]
    },
    {
      "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 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": "readBismark2PC",
      "title": "Read Bismark Coverage Files",
      "concept": [
        "Reading data files",
        "Differential methylation"
      ],
      "topics": [
        "readBismark2PC"
      ]
    },
    {
      "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",
      "concept": [
        "Preprocessing"
      ],
      "topics": [
        "rowsum.DGEList",
        "rowsum.PCList",
        "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": [
        "Classes"
      ],
      "topics": [
        "SE2DGEList"
      ]
    },
    {
      "page": "Seurat2PB",
      "title": "Seurat or SeuratObject Class Object to Pseudo-Bulk DGEList",
      "concept": [
        "Classes"
      ],
      "topics": [
        "Seurat2PB"
      ]
    },
    {
      "page": "spliceVariants",
      "title": "Identify Genes with Splice Variants (Classic Pipeline)",
      "concept": [
        "Differential usage"
      ],
      "topics": [
        "spliceVariants"
      ]
    },
    {
      "page": "splitGencodeTxNames",
      "title": "Split GENCODE Transcript Names and Summarize By Gene",
      "concept": [
        "Transcript expression",
        "Reading data files"
      ],
      "topics": [
        "collapseGencodeTx2Gene",
        "splitGencodeTxNames"
      ]
    },
    {
      "page": "splitIntoGroups",
      "title": "Split the Counts or Pseudocounts from a DGEList Object According to Group",
      "topics": [
        "splitIntoGroups",
        "splitIntoGroups.default",
        "splitIntoGroups.DGEList",
        "splitIntoGroupsPseudo"
      ]
    },
    {
      "page": "subsetting",
      "title": "Subset DGEList, PCList, DGEGLM, DGEExact and DGELRT Objects",
      "concept": [
        "Classes"
      ],
      "topics": [
        "subsetting",
        "[.DGEBIN",
        "[.DGEExact",
        "[.DGEGLM",
        "[.DGEList",
        "[.DGELRT",
        "[.PCList",
        "[.TopTags"
      ]
    },
    {
      "page": "sumTechReps",
      "title": "Sum over Replicate Samples",
      "concept": [
        "Preprocessing"
      ],
      "topics": [
        "sumTechReps",
        "sumTechReps.default",
        "sumTechReps.DGEList",
        "sumTechReps.SummarizedExperiment"
      ]
    },
    {
      "page": "systematicSubset",
      "title": "Take a Systematic Subset of Indices",
      "topics": [
        "systematicSubset"
      ]
    },
    {
      "page": "thinCounts",
      "title": "Binomial or Multinomial Thinning of Counts",
      "concept": [
        "Preprocessing"
      ],
      "topics": [
        "thinCounts"
      ]
    },
    {
      "page": "topSpliceDGE",
      "title": "Top Table of Differentially Spliced Genes or Exons",
      "topics": [
        "topSpliceDGE"
      ]
    },
    {
      "page": "topTags",
      "title": "Table of the Top Differentially Expressed Genes/Tags",
      "topics": [
        "show,TopTags-method",
        "topTags",
        "TopTags-class"
      ]
    },
    {
      "page": "tpm",
      "title": "Transcripts per Million",
      "concept": [
        "Differential usage"
      ],
      "topics": [
        "tpm"
      ]
    },
    {
      "page": "tpmProp",
      "title": "TPM Proportion by Transcript for Each Gene",
      "concept": [
        "Differential usage"
      ],
      "topics": [
        "tpmProp"
      ]
    },
    {
      "page": "validDGEList",
      "title": "Check for Valid DGEList Object",
      "concept": [
        "Classes"
      ],
      "topics": [
        "validDGEList"
      ]
    },
    {
      "page": "weightedCondLogLikDerDelta",
      "title": "Weighted Conditional Log-Likelihood in Terms of Delta",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "weightedCondLogLikDerDelta"
      ]
    },
    {
      "page": "WLEB",
      "title": "Weighted Likelihood Empirical Bayes",
      "concept": [
        "Dispersion estimation"
      ],
      "topics": [
        "WLEB"
      ]
    },
    {
      "page": "zscoreNBinom",
      "title": "Z-score Equivalents of Negative Binomial Deviate",
      "concept": [
        "Gene set tests"
      ],
      "topics": [
        "zscoreNBinom"
      ]
    }
  ],
  "_rundeps": [
    "limma",
    "statmod"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "intro.Rmd",
      "filename": "intro.html",
      "title": "A brief introduction to edgeR",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What is it?",
        "How to get help",
        "Further reading"
      ],
      "created": "2023-06-21 10:09:59",
      "modified": "2025-12-23 06:09:34",
      "commits": 3
    },
    {
      "source": "edgeRUsersGuide.Rnw",
      "filename": "edgeRUsersGuide.pdf",
      "title": "edgeR User's Guide",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2023-06-20 00:55:03",
      "modified": "2023-06-20 00:55:03",
      "commits": 1
    }
  ],
  "_score": 13.789311381972352,
  "_indexed": true,
  "_nocasepkg": "edger",
  "_universes": [
    "bioc",
    "yunshun"
  ],
  "_previous": "4.99.10",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.99.11",
      "date": "2026-10-31T22:28:53.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/a25b8fc6b8d1904f03f83067e243f87366bb817c2aa1ace13d9a1c11f5d21f2a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.99.11",
      "date": "2026-10-31T22:30:17.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/2e34af214a0eef60201c5bb3c7e2cc064b62dddadf772c4df85dc466781651e8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "4.99.11",
      "date": "2026-10-31T22:28:53.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/409e2b92a7b3450916d6cd0b81e02d441ac7046dcc0b8fc9c80d536e7461e3a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "4.99.11",
      "date": "2026-10-31T22:29:50.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/021827ecad8827ad904cb4e82748b64a6034d924a50bc126026c5b1c835e76e6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.99.11",
      "date": "2026-10-31T22:41:53.000Z",
      "arch": "aarch64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/de712f3158d81ad087ce3183ec697478970c12c1e51bd0f0276bcc79b978d898",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.99.11",
      "date": "2026-10-31T22:34:54.000Z",
      "arch": "x86_64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/4c81a0d64caab23d8f61e9b890fbc8a1a83e23643a777c48af8faa2f3c252c28",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "4.99.11",
      "date": "2026-10-31T22:36:56.000Z",
      "arch": "aarch64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/fe70929e00ea9ee38db520cc36aa556ee5b6e5f84de5fb113e1b6e5ef97a0c71",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "4.99.11",
      "date": "2026-10-31T22:37:01.000Z",
      "arch": "x86_64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/8648eb46a3871e45726b30d1f428a1199a2a0d0cc207c7b55d377ec92df6f43f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "4.99.11",
      "date": "2026-10-31T22:28:44.000Z",
      "arch": "emscripten",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/27b195f01a1f39991c1c4a6799e5cd911a45117fef1cceaec5ec5376baffc9d2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "4.99.11",
      "date": "2026-10-31T22:29:58.000Z",
      "arch": "aarch64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/fe69c32329380990190231ea66eaa1c84e9371c2fd7d6da59c2ec2c2e432ca4d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "4.99.11",
      "date": "2026-10-31T22:28:16.000Z",
      "arch": "x86_64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/5f6451d46b865edeb47ef92bc34a5b272b2d7ffcc8f5b6b379e204cbdee05d8c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "4.99.11",
      "date": "2026-10-31T22:28:22.000Z",
      "arch": "x86_64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/2d58e98ca6b93ccfcb3084038b1582e81692b78f7de29095d257c545717a7124",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "4.99.11",
      "date": "2026-10-31T22:29:59.000Z",
      "arch": "aarch64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/ed7e19de9d94fcadc7acad51ac03099ddf8a8e3e065188015479c97d6f034417",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "4.99.11",
      "date": "2026-10-31T22:28:14.000Z",
      "arch": "x86_64",
      "commit": "c708c74473eb7781078133cb51a4f0ffa77f3b67",
      "fileid": "https://r2.ropensci.org/4c1f5d18733de1efb456dda31fbbf1e80afbf03c67d1d1d57caec8af4f705b08",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41247873548"
    }
  ]
}