{
  "_id": "6a1ace2a1d7bb097a09dfa58",
  "Package": "geva",
  "Type": "Package",
  "Title": "Gene Expression Variation Analysis (GEVA)",
  "Description": "Statistic methods to evaluate variations of differential\nexpression (DE) between multiple biological conditions. It\ntakes into account the fold-changes and p-values from previous\ndifferential expression (DE) results that use large-scale data\n(*e.g.*, microarray and RNA-seq) and evaluates which genes\nwould react in response to the distinct experiments. This\nevaluation involves an unique pipeline of statistical methods,\nincluding weighted summarization, quantile detection, cluster\nanalysis, and ANOVA tests, in order to classify a subset of\nrelevant genes whose DE is similar or dependent to certain\nbiological factors.",
  "Version": "1.21.0",
  "Authors@R": "c(person(given = \"Itamar José\",\nfamily = \"Guimarães Nunes\",\nrole = c(\"aut\", \"cre\"),\nemail = \"nunesijg@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6246-4658\")),\nperson(given = \"Murilo\",\nfamily = \"Zanini David\",\nemail = \"zanini.murilo@gmail.com\",\nrole = \"ctb\"),\nperson(given = \"Bruno\",\nfamily = \"César Feltes\",\nemail = \"bcfeltes@gmail.com\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2825-8295\")),\nperson(given = \"Marcio\",\nfamily = \"Dorn\",\nemail = \"mdorn@inf.ufrgs.br\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0001-8534-3480\")))",
  "URL": "https://github.com/sbcblab/geva",
  "BiocType": "Software",
  "biocViews": "Classification, DifferentialExpression, GeneExpression,\nMicroarray, MultipleComparison, RNASeq, SystemsBiology,\nTranscriptomics",
  "License": "LGPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Collate": "'stringhelpers.R' 'callhelpers.R' 'vectorhelpers.R'\n'printhelpers.R' 'asserts.R' 'usecasechecks.R' 'plotting.R'\n'dochelpers.R' 'generics.R' 'classhelpers.R' 'c_SVTable.R'\n'c_GEVAGroupSet.R' 'c_GEVACluster.R' 'funhelpers.R' 'linq.R'\n'c_TypedList.R' 'c_SVAttribute.R' 'c_GEVAInput.R'\n'c_GEVASummary.R' 'c_GEVAGroupedSummary.R' 'c_GEVAQuantiles.R'\n'c_GEVAQuantilesAdjusted.R' 'c_GEVAResults.R' 'summarization.R'\n'clusteringbase.R' 'matrixhelpers.R' 'statmath.R'\n'dclustering.R' 'quantiles.R' 'factoring.R' 'scoremerge.R'\n'finalize.R' 'geva-package.R' 'hclustering.R' 'idealtesting.R'\n'input.R'",
  "Config/testthat/edition": "3",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:17 UTC",
  "RemoteUrl": "https://github.com/bioc/geva",
  "RemoteRef": "HEAD",
  "RemoteSha": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:13:05 UTC",
    "User": "root"
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  "Author": "Itamar José Guimarães Nunes [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6246-4658>),\nMurilo Zanini David [ctb],\nBruno César Feltes [ctb] (ORCID:\n<https://orcid.org/0000-0002-2825-8295>),\nMarcio Dorn [ctb] (ORCID: <https://orcid.org/0000-0001-8534-3480>)",
  "Maintainer": "Itamar José Guimarães Nunes <nunesijg@gmail.com>",
  "MD5sum": "30a7e545aca39ffc4cfddcd7b9549bcc",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-30T08:13:05.000Z",
  "_published": "2026-05-30T11:46:50.028Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678853250",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/geva",
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    "id": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260",
    "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",
    "time": 1777380917
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  "_selfowned": true,
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  "_updates": [
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    "differentialexpression",
    "geneexpression",
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    "multiplecomparison",
    "rnaseq",
    "systemsbiology",
    "transcriptomics"
  ],
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/geva"
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  "_devurl": "https://github.com/sbcblab/geva",
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    "extra/citation.json",
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    "manual.pdf"
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  "_homeurl": "https://github.com/sbcblab/geva",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "analysis.params",
    "as.SVTable",
    "centroids",
    "classification.table",
    "classification.table<-",
    "cluster.method",
    "elem.class",
    "elem.class<-",
    "factors",
    "factors<-",
    "featureTable",
    "featureTable<-",
    "get.distance.method",
    "get.summary.method",
    "get.variation.method",
    "geva.cluster",
    "geva.dcluster",
    "geva.finalize",
    "geva.hcluster",
    "geva.ideal.example",
    "geva.input.correct",
    "geva.input.filter",
    "geva.input.rename.rows",
    "geva.merge.input",
    "geva.quantiles",
    "geva.quick",
    "geva.read.tables",
    "geva.summarize",
    "group.rels",
    "groups",
    "groupsets",
    "groupsets<-",
    "infolist",
    "infolist<-",
    "inputdata",
    "inputnames",
    "inputvalues",
    "inputweights",
    "offsets",
    "options.cl.score.method",
    "options.cluster.method",
    "options.dcluster.method",
    "options.distance",
    "options.factoring.p.adjust",
    "options.hc.method",
    "options.hc.metric",
    "options.quantiles",
    "options.summary",
    "options.variation",
    "plot",
    "qareasizes",
    "qcount",
    "qindexes",
    "quantiles",
    "quantiles.method",
    "results.table",
    "scores",
    "show",
    "sv",
    "sv.data",
    "sv.scores",
    "svattr",
    "svtable",
    "top.genes",
    "typed.list",
    "variation"
  ],
  "_help": [
    {
      "page": "generics",
      "title": "GEVA Generic Methods",
      "topics": [
        "analysis.params",
        "as.SVTable",
        "centroids",
        "classification.table",
        "classification.table<-",
        "cluster.method",
        "elem.class",
        "elem.class<-",
        "factors",
        "factors<-",
        "featureTable",
        "featureTable<-",
        "generics",
        "get.distance.method",
        "get.summary.method",
        "get.variation.method",
        "group.rels",
        "groups",
        "groupsets",
        "groupsets<-",
        "infolist",
        "infolist<-",
        "inputdata",
        "inputnames",
        "inputvalues",
        "inputweights",
        "offsets",
        "qareasizes",
        "qcount",
        "qindexes",
        "quantiles",
        "quantiles.method",
        "results.table",
        "scores",
        "sv",
        "sv.data",
        "sv.scores",
        "svattr",
        "variation"
      ]
    },
    {
      "page": "geva.cluster",
      "title": "GEVA Cluster Analysis",
      "concept": [
        "geva.cluster"
      ],
      "topics": [
        "geva.cluster",
        "options.cl.score.method",
        "options.cluster.method",
        "options.distance"
      ]
    },
    {
      "page": "geva.dcluster",
      "title": "GEVA Density Clustering",
      "concept": [
        "geva.cluster"
      ],
      "topics": [
        "geva.dcluster",
        "options.dcluster.method"
      ]
    },
    {
      "page": "geva.finalize",
      "title": "Concatenating GEVA calculations into the final results",
      "topics": [
        "geva.finalize",
        "options.factoring.p.adjust"
      ]
    },
    {
      "page": "geva.hcluster",
      "title": "GEVA Hierarchical Clustering",
      "concept": [
        "geva.cluster"
      ],
      "topics": [
        "geva.hcluster",
        "options.hc.method",
        "options.hc.metric"
      ]
    },
    {
      "page": "geva.ideal.example",
      "title": "GEVA ``Ideal'' Example for Package Testing",
      "topics": [
        "geva.ideal.example"
      ]
    },
    {
      "page": "geva.input.correct",
      "title": "GEVA Input Post-processing",
      "topics": [
        "geva.input.correct",
        "geva.input.filter",
        "geva.input.rename.rows"
      ]
    },
    {
      "page": "geva.merge.input",
      "title": "GEVA Input Processing and Merge",
      "topics": [
        "geva.merge.input",
        "geva.read.tables"
      ]
    },
    {
      "page": "geva.quantiles",
      "title": "GEVA Quantiles Detection",
      "concept": [
        "geva.cluster"
      ],
      "topics": [
        "geva.quantiles",
        "options.quantiles"
      ]
    },
    {
      "page": "geva.quick",
      "title": "All-In-One Function for GEVA Intermediate Procedures",
      "topics": [
        "geva.quick"
      ]
    },
    {
      "page": "geva.summarize",
      "title": "Summarizes the GEVAInput",
      "topics": [
        "geva.summarize",
        "options.summary",
        "options.variation"
      ]
    },
    {
      "page": "GEVACluster-class",
      "title": "GEVA Clustering Results",
      "topics": [
        "cluster.method,GEVACluster-method",
        "GEVACluster-class",
        "lines.GEVACluster",
        "plot,GEVACluster,SVTable-method",
        "show,GEVACluster-method"
      ]
    },
    {
      "page": "GEVAGroupedSummary-class",
      "title": "GEVA Grouped Summary-Variation Table",
      "topics": [
        "analysis.params,GEVAGroupedSummary-method",
        "as.expression.GEVAGroupedSummary",
        "as.matrix.GEVAGroupedSummary",
        "cluster.method,GEVAGroupedSummary-method",
        "GEVAGroupedSummary-class",
        "groupsets,GEVAGroupedSummary-method",
        "groupsets<-,GEVAGroupedSummary,GEVAGroupSet-method",
        "lines.GEVAGroupedSummary",
        "plot,GEVAGroupedSummary,missing-method",
        "points.GEVAGroupedSummary",
        "quantiles,GEVAGroupedSummary-method",
        "show,GEVAGroupedSummary-method"
      ]
    },
    {
      "page": "GEVAGroupSet-class",
      "title": "GEVA Grouping Results",
      "topics": [
        "analysis.params,GEVAGroupSet-method",
        "as.data.frame.GEVAGroupSet",
        "as.expression.GEVAGroupSet",
        "as.SVTable.GEVAGroupSet",
        "centroids,GEVAGroupSet-method",
        "classification.table,GEVAGroupSet-method",
        "classification.table<-,GEVAGroupSet,data.frame-method",
        "cluster.method,GEVAGroupSet-method",
        "color.values.GEVAGroupSet",
        "featureTable,GEVAGroupSet-method",
        "GEVAGroupSet-class",
        "groups,GEVAGroupSet-method",
        "infolist,GEVAGroupSet,character-method",
        "infolist,GEVAGroupSet,missing-method",
        "infolist<-,GEVAGroupSet,list-method",
        "length,GEVAGroupSet-method",
        "levels.GEVAGroupSet",
        "names,GEVAGroupSet-method",
        "offsets,GEVAGroupSet-method",
        "plot,GEVAGroupSet,GEVAGroupSet-method",
        "plot,GEVAGroupSet,missing-method",
        "plot,GEVAGroupSet,SVTable-method",
        "plot,SVTable,GEVAGroupSet-method",
        "points.GEVAGroupSet",
        "scores,GEVAGroupSet,character-method",
        "scores,GEVAGroupSet,missing-method",
        "show,GEVAGroupSet-method",
        "sv,GEVAGroupSet-method",
        "sv.data,GEVAGroupSet-method"
      ]
    },
    {
      "page": "GEVAInput-class",
      "title": "GEVA Input Data",
      "topics": [
        "analysis.params,GEVAInput-method",
        "as.array.GEVAInput",
        "dim,GEVAInput-method",
        "dimnames,GEVAInput-method",
        "dimnames<-,GEVAInput,list-method",
        "factors,GEVAInput-method",
        "factors<-,GEVAInput,character-method",
        "factors<-,GEVAInput,factor-method",
        "featureTable,GEVAInput-method",
        "featureTable<-,GEVAInput,data.frame-method",
        "GEVAInput-class",
        "head.GEVAInput",
        "infolist,GEVAInput,character-method",
        "infolist,GEVAInput,missing-method",
        "infolist<-,GEVAInput,list-method",
        "inputdata,GEVAInput-method",
        "inputnames,GEVAInput-method",
        "inputvalues,GEVAInput-method",
        "inputweights,GEVAInput,logical-method",
        "inputweights,GEVAInput,missing-method",
        "length,GEVAInput-method",
        "levels.GEVAInput",
        "names,GEVAInput-method",
        "plot,GEVAInput,missing-method",
        "show,GEVAInput-method",
        "tail.GEVAInput",
        "[,GEVAInput,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "GEVAQuantiles-class",
      "title": "GEVA Quantiles Grouping Results",
      "topics": [
        "as.expression.GEVAQuantiles",
        "as.SVTable.GEVAQuantiles",
        "classification.table,GEVAQuantiles-method",
        "classification.table<-,GEVAQuantiles,data.frame-method",
        "cluster.method,GEVAQuantiles-method",
        "dim,GEVAQuantiles-method",
        "GEVAQuantiles-class",
        "lines.GEVAQuantiles",
        "plot,GEVAQuantiles,SVTable-method",
        "qareasizes,GEVAQuantiles-method",
        "qcount,GEVAQuantiles-method",
        "qindexes,GEVAQuantiles-method",
        "quantiles,GEVAQuantiles-method",
        "quantiles.method,GEVAQuantiles-method",
        "show,GEVAQuantiles-method",
        "sv.scores,GEVAQuantiles-method",
        "[,GEVAQuantiles,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "GEVAQuantilesAdjusted-class",
      "title": "GEVA Adjusted Quantiles Results",
      "topics": [
        "GEVAQuantilesAdjusted-class",
        "group.rels,GEVAQuantilesAdjusted-method",
        "show,GEVAQuantilesAdjusted-method"
      ]
    },
    {
      "page": "GEVAResults-class",
      "title": "GEVA Results Table",
      "topics": [
        "$,GEVAResults-method",
        "analysis.params,GEVAResults-method",
        "as.expression.GEVAResults",
        "dim,GEVAResults-method",
        "dimnames,GEVAResults-method",
        "featureTable,GEVAResults-method",
        "GEVAResults-class",
        "head.GEVAResults",
        "infolist,GEVAResults,character-method",
        "infolist,GEVAResults,missing-method",
        "inputdata,GEVAResults-method",
        "inputvalues,GEVAResults-method",
        "inputweights,GEVAResults,logical-method",
        "inputweights,GEVAResults,missing-method",
        "length,GEVAResults-method",
        "levels.GEVAResults",
        "names,GEVAResults-method",
        "plot,GEVAResults,missing-method",
        "points.GEVAResults",
        "quantiles,GEVAResults-method",
        "results.table,GEVAResults-method",
        "show,GEVAResults-method",
        "sv,GEVAResults-method",
        "sv.data,GEVAResults-method",
        "[,GEVAResults,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "GEVASummary-class",
      "title": "GEVA Summary-Variation Table",
      "topics": [
        "analysis.params,GEVASummary-method",
        "as.expression.GEVASummary",
        "as.matrix.GEVASummary",
        "factors,GEVASummary-method",
        "factors<-,GEVASummary,character-method",
        "factors<-,GEVASummary,factor-method",
        "featureTable,GEVASummary-method",
        "get.summary.method.GEVASummary",
        "get.variation.method.GEVASummary",
        "GEVASummary-class",
        "groupsets,GEVASummary-method",
        "groupsets<-,GEVASummary,GEVAGroupSet-method",
        "groupsets<-,GEVASummary,TypedList-method",
        "infolist,GEVASummary,missing-method",
        "infolist<-,GEVASummary,list-method",
        "inputdata,GEVASummary-method",
        "inputnames,GEVASummary-method",
        "inputvalues,GEVASummary-method",
        "inputweights,GEVASummary,logical-method",
        "inputweights,GEVASummary,missing-method",
        "plot,GEVASummary,missing-method",
        "quantiles,GEVASummary-method",
        "show,GEVASummary-method"
      ]
    },
    {
      "page": "SVAttribute-class",
      "title": "Summary-Variation Attribute Field",
      "topics": [
        "$,SVAttribute-method",
        "as.character.SVAttribute",
        "as.vector.SVAttribute",
        "dim,SVAttribute-method",
        "names,SVAttribute-method",
        "show,SVAttribute-method",
        "summary.SVAttribute",
        "sv,SVAttribute-method",
        "sv.data,SVAttribute-method",
        "svattr,character,character-method",
        "svattr,integer,integer-method",
        "svattr,numeric,numeric-method",
        "SVAttribute",
        "SVAttribute-class",
        "SVChrAttribute",
        "SVChrAttribute-class",
        "SVIntAttribute",
        "SVIntAttribute-class",
        "SVNumAttribute",
        "SVNumAttribute-class",
        "variation.SVAttribute",
        "[,SVAttribute,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "SVTable-class",
      "title": "Summary-Variation Table",
      "topics": [
        "$,SVTable-method",
        "as.data.frame.SVTable",
        "as.matrix.SVTable",
        "as.SVTable.data.frame",
        "as.SVTable.matrix",
        "as.SVTable.SVTable",
        "dim,SVTable-method",
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    },
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      "page": "top.genes",
      "title": "Top Results from GEVA",
      "topics": [
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      ]
    },
    {
      "page": "TypedList-class",
      "title": "Type-strict List (TypedList-class)",
      "topics": [
        "as.list.TypedList",
        "as.typed.list.list",
        "as.typed.list.TypedList",
        "as.typed.list.vector",
        "elem.class,TypedList-method",
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        "show,TypedList-method",
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  "_rundeps": [
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    "fastcluster",
    "generics",
    "matrixStats",
    "Rcpp"
  ],
  "_vignettes": [
    {
      "source": "geva.Rmd",
      "filename": "geva.html",
      "title": "Gene Expression Variation Analysis (GEVA)",
      "author": "Itamar José Guimarães Nunes^[Structural Bioinformatics and Computational Lab (SBCB) -- Federal University of Rio Grande do Sul (UFRGS)], Murilo Zanini David^[Graduate Program in Ecology -- Federal University of Rio Grande do Sul (UFRGS)], \\linebreak, Bruno César Feltes\\footnotemark[1], and Marcio Dorn\\footnotemark[1]",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Data input",
        "Alternative 1 -- Tab-delimited Text Files",
        "Alternative 2 -- Multiple table objects",
        "Alternative 3 -- Results from limma",
        "Alternative 4 -- Ideal input data (for tests only)",
        "Input data post-processing (optional)",
        "Numeric table correcting",
        "Filtering values below statistical significance",
        "Renaming the row names",
        "SV Analyses",
        "Summarization",
        "Makes a safe copy of the summary data",
        "Appends the quantiles data",
        "Appends the clustered data",
        "Draws a SV plot with grouped highlights (optional)",
        "Alternative 2 -- With factors",
        "Shortcut function and reanalysis"
      ],
      "created": "2021-01-20 16:57:58",
      "modified": "2021-03-10 00:15:24",
      "commits": 6
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  "_nocasepkg": "geva",
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