{
  "_id": "6a493aeba19c9318096e6d76",
  "Package": "DRIMSeq",
  "Type": "Package",
  "Title": "Differential transcript usage and tuQTL analyses with\nDirichlet-multinomial model in RNA-seq",
  "Version": "1.41.0",
  "Date": "2017-05-24",
  "Authors@R": "c(person(given = \"Malgorzata\", family = \"Nowicka\", \nrole = c(\"aut\", \"cre\"),\nemail = \"gosia.nowicka.uzh@gmail.com\"))",
  "Description": "The package provides two frameworks. One for the\ndifferential transcript usage analysis between different\nconditions and one for the tuQTL analysis. Both are based on\nmodeling the counts of genomic features (i.e., transcripts)\nwith the Dirichlet-multinomial distribution. The package also\nmakes available functions for visualization and exploration of\nthe data and results.",
  "biocViews": "ImmunoOncology, SNP, AlternativeSplicing,\nDifferentialSplicing, Genetics, RNASeq, Sequencing,\nWorkflowStep, MultipleComparison, GeneExpression,\nDifferentialExpression",
  "License": "GPL (>= 3)",
  "ByteCompile": "false",
  "VignetteBuilder": "knitr",
  "Collate": "'DRIMSeq.R' 'class_show_utils.R' 'class_MatrixList.R'\n'class_dmDSdata.R' 'class_dmDSprecision.R' 'class_dmDSfit.R'\n'class_dmDStest.R' 'class_dmSQTLdata.R'\n'class_dmSQTLprecision.R' 'class_dmSQTLfit.R'\n'class_dmSQTLtest.R' 'dmDS_CRadjustment.R'\n'dmDS_estimateCommonPrecision.R'\n'dmDS_estimateTagwisePrecision.R' 'dmDS_filter.R' 'dmDS_fit.R'\n'dmDS_profileLik.R' 'dmSQTL_CRadjustment.R'\n'dmSQTL_estimateCommonPrecision.R'\n'dmSQTL_estimateTagwisePrecision.R' 'dmSQTL_filter.R'\n'dmSQTL_fit.R' 'dmSQTL_permutations.R' 'dmSQTL_profileLik.R'\n'dm_CRadjustmentManyGroups.R' 'dm_CRadjustmentOneGroup.R'\n'dm_CRadjustmentRegression.R' 'dm_LRT.R' 'dm_core_Hessian.R'\n'dm_core_colorb.R' 'dm_core_deviance.R' 'dm_core_lik.R'\n'dm_core_score.R' 'dm_estimateMeanExpression.R'\n'dm_fitManyGroups.R' 'dm_fitOneGroup.R' 'dm_fitRegression.R'\n'dm_plotData.R' 'dm_plotPrecision.R' 'dm_plotProportions.R'\n'dm_plotPvalues.R' 'dm_profileLikModeration.R'",
  "RoxygenNote": "6.0.1",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:03 UTC",
  "RemoteUrl": "https://github.com/bioc/DRIMSeq",
  "RemoteRef": "HEAD",
  "RemoteSha": "47ade4497ccde94343ddde3016a7ce770c446286",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 16:48:31 UTC",
    "User": "root"
  },
  "Author": "Malgorzata Nowicka [aut, cre]",
  "Maintainer": "Malgorzata Nowicka <gosia.nowicka.uzh@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "DRIMSeq_1.41.0.tar.gz",
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  "_created": "2026-07-04T16:48:31.000Z",
  "_published": "2026-07-04T16:55:07.855Z",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 10
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28712857417",
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  "_upstream": "https://github.com/bioc/DRIMSeq",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "name": "Malgorzata Nowicka",
    "email": "gosia.nowicka.uzh@gmail.com",
    "login": "gosianow",
    "description": "",
    "uuid": 6965465
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
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      "week": "2025-44",
      "n": 2
    },
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  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
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    "snp",
    "alternativesplicing",
    "differentialsplicing",
    "genetics",
    "rnaseq",
    "sequencing",
    "workflowstep",
    "multiplecomparison",
    "geneexpression",
    "differentialexpression"
  ],
  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_searchresults": 242,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DRIMSeq.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "coefficients",
    "colnames",
    "colnames<-",
    "common_precision",
    "common_precision<-",
    "counts",
    "design",
    "dmDSdata",
    "dmFilter",
    "dmFit",
    "dmPrecision",
    "dmSQTLdata",
    "dmTest",
    "elementNROWS",
    "genewise_precision",
    "genewise_precision<-",
    "mean_expression",
    "ncol",
    "nrow",
    "plotData",
    "plotPrecision",
    "plotProportions",
    "plotPValues",
    "proportions",
    "results",
    "rownames",
    "rownames<-",
    "samples"
  ],
  "_help": [
    {
      "page": "dm_plotDataDSInfo",
      "title": "Plot the frequency of present features",
      "topics": [
        "dm_plotDataDSInfo"
      ]
    },
    {
      "page": "dm_plotProportions",
      "title": "Plot feature proportions",
      "topics": [
        "dm_plotProportions"
      ]
    },
    {
      "page": "dmDSdata",
      "title": "Create dmDSdata object",
      "topics": [
        "dmDSdata"
      ]
    },
    {
      "page": "dmDSdata-class",
      "title": "dmDSdata object",
      "topics": [
        "counts,dmDSdata-method",
        "dmDSdata-class",
        "length,dmDSdata-method",
        "names,dmDSdata-method",
        "samples",
        "samples,dmDSdata-method",
        "[,dmDSdata,ANY-method",
        "[,dmDSdata-method"
      ]
    },
    {
      "page": "dmDSfit-class",
      "title": "dmDSfit object",
      "topics": [
        "coefficients,dmDSfit-method",
        "design,dmDSfit-method",
        "dmDSfit-class",
        "proportions",
        "proportions,dmDSfit-method"
      ]
    },
    {
      "page": "dmDSprecision-class",
      "title": "dmDSprecision object",
      "topics": [
        "common_precision",
        "common_precision,dmDSprecision-method",
        "common_precision<-",
        "common_precision<-,dmDSprecision-method",
        "design,dmDSprecision-method",
        "dmDSprecision-class",
        "genewise_precision",
        "genewise_precision,dmDSprecision-method",
        "genewise_precision<-",
        "genewise_precision<-,dmDSprecision-method",
        "mean_expression",
        "mean_expression,dmDSprecision-method"
      ]
    },
    {
      "page": "dmDStest-class",
      "title": "dmDStest object",
      "topics": [
        "design,dmDStest-method",
        "dmDStest-class",
        "results",
        "results,dmDStest-method"
      ]
    },
    {
      "page": "dmFilter",
      "title": "Filtering",
      "topics": [
        "dmFilter",
        "dmFilter,dmDSdata-method",
        "dmFilter,dmSQTLdata-method"
      ]
    },
    {
      "page": "dmFit",
      "title": "Fit the Dirichlet-multinomial and/or the beta-binomial full model regression",
      "topics": [
        "dmFit",
        "dmFit,dmDSprecision-method",
        "dmFit,dmSQTLprecision-method"
      ]
    },
    {
      "page": "dmPrecision",
      "title": "Estimate the precision parameter in the Dirichlet-multinomial model",
      "topics": [
        "dmPrecision",
        "dmPrecision,dmDSdata-method",
        "dmPrecision,dmSQTLdata-method"
      ]
    },
    {
      "page": "dmSQTLdata",
      "title": "Create dmSQTLdata object",
      "topics": [
        "dmSQTLdata"
      ]
    },
    {
      "page": "dmSQTLdata-class",
      "title": "dmSQTLdata object",
      "topics": [
        "counts,dmSQTLdata-method",
        "dmSQTLdata-class",
        "length,dmSQTLdata-method",
        "names,dmSQTLdata-method",
        "samples,dmSQTLdata-method",
        "[,dmSQTLdata,ANY-method",
        "[,dmSQTLdata-method"
      ]
    },
    {
      "page": "dmSQTLfit-class",
      "title": "dmSQTLfit object",
      "topics": [
        "dmSQTLfit-class"
      ]
    },
    {
      "page": "dmSQTLprecision-class",
      "title": "dmSQTLprecision object",
      "topics": [
        "common_precision,dmSQTLprecision-method",
        "dmSQTLprecision-class",
        "genewise_precision,dmSQTLprecision-method",
        "mean_expression,dmSQTLprecision-method"
      ]
    },
    {
      "page": "dmSQTLtest-class",
      "title": "dmSQTLtest object",
      "topics": [
        "dmSQTLtest-class",
        "results,dmSQTLtest-method"
      ]
    },
    {
      "page": "dmTest",
      "title": "Likelihood ratio test to detect differential transcript/exon usage",
      "topics": [
        "dmTest",
        "dmTest,dmDSfit-method",
        "dmTest,dmSQTLfit-method"
      ]
    },
    {
      "page": "MatrixList-class",
      "title": "MatrixList object",
      "topics": [
        "$,MatrixList-method",
        "colnames,MatrixList-method",
        "colnames<-,MatrixList-method",
        "dim,MatrixList-method",
        "elementNROWS,MatrixList-method",
        "length,MatrixList-method",
        "MatrixList-class",
        "names,MatrixList-method",
        "names<-,MatrixList-method",
        "ncol,MatrixList-method",
        "nrow,MatrixList-method",
        "rownames,MatrixList-method",
        "rownames<-,MatrixList-method",
        "[,MatrixList,ANY-method",
        "[,MatrixList-method",
        "[[,MatrixList-method"
      ]
    },
    {
      "page": "plotData",
      "title": "Plot data summary",
      "topics": [
        "plotData",
        "plotData,dmDSdata-method",
        "plotData,dmSQTLdata-method"
      ]
    },
    {
      "page": "plotPrecision",
      "title": "Precision versus mean expression plot",
      "topics": [
        "plotPrecision",
        "plotPrecision,dmDSprecision-method",
        "plotPrecision,dmSQTLprecision-method"
      ]
    },
    {
      "page": "plotProportions",
      "title": "Plot feature proportions",
      "topics": [
        "plotProportions",
        "plotProportions,dmDSfit-method",
        "plotProportions,dmSQTLfit-method"
      ]
    },
    {
      "page": "plotPValues",
      "title": "Plot p-value distribution",
      "topics": [
        "plotPValues",
        "plotPValues,dmDStest-method",
        "plotPValues,dmSQTLtest-method"
      ]
    }
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      "source": "DRIMSeq.Rnw",
      "filename": "DRIMSeq.pdf",
      "title": "Differential transcript usage and transcript usage QTL analyses in RNA-seq with the DRIMSeq package",
      "engine": "knitr::knitr",
      "headings": [
        "1 Main changes in the DRIMSeq package",
        "2 Overview of the Dirichlet-multinomial model",
        "3 Important notes",
        "4 Hints for DRIMSeq pipelines",
        "5 Differential transcript usage analysis workflow",
        "6 tuQTL analysis workflow",
        "7 Session information"
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      "created": "2016-03-23 22:36:02",
      "modified": "2017-08-22 13:28:29",
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