{ "_id": "6aeb3678818c9e3ef6dc1721", "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": "2026-11-04 13:37:42 UTC", "User": "root" }, "Author": "Itamar José Guimarães Nunes [aut, cre] (ORCID:\n),\nMurilo Zanini David [ctb],\nBruno César Feltes [ctb] (ORCID:\n),\nMarcio Dorn [ctb] (ORCID: )", "Maintainer": "Itamar José Guimarães Nunes ", "_user": "bioc", "_type": "src", "_file": "geva_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/fa28f041f11f35f1c2e280badb0acf750a8805bb22d5eea557290f1f315e2cdc", "_filesize": 5754413, "_sha256": "fa28f041f11f35f1c2e280badb0acf750a8805bb22d5eea557290f1f315e2cdc", "_expires": "2027-02-12T13:43:17.000Z", "_created": "2026-11-04T13:37:42.000Z", "_published": "2026-11-04T13:43:20.186Z", "_upstream": "https://github.com/bioc/geva", "_status": "success", "_maintainer": { "name": "Itamar José Guimarães Nunes", "email": "nunesijg@gmail.com", "login": "nunesijg", "description": "", "uuid": 51794955, "orcid": "0000-0002-6246-4658" }, "_jobs": [ { "job": 126608386701, "time": 165, "config": "bioc-checks", "r": "4.6.2", "check": "WARNING", "artifact": "13329270017" }, { "job": 126608386610, "time": 257, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13328306985" }, { "job": 126608386821, "time": 293, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13328601774" }, { "job": 126608386649, "time": 187, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13329090215" }, { "job": 126608386460, "time": 161, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13328103857" }, { "job": 126605873872, "time": 278, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13326714670" }, { "job": 126608386390, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13327894548" }, { "job": 126608386899, "time": 160, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13329120105" }, { "job": 126608386793, "time": 223, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13327564910" }, { "job": 126608386734, "time": 221, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13327664390" } ], "_bioccheck": { "error": 0, "warning": 5, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227", "_commit": { "id": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380917 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "dbscan", "role": "Imports" }, { "package": "fastcluster", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "devtools", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "topGO", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "classification", "differentialexpression", "geneexpression", "microarray", "multiplecomparison", "rnaseq", "systemsbiology", "transcriptomics" ], "_stars": 2, "_contributors": [ { "user": "nunesijg", "count": 69, "uuid": 51794955 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 484, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 405, "source": "https://www.bioconductor.org/packages/stats/bioc/geva" }, "_devurl": "https://github.com/sbcblab/geva", "_searchresults": 4, "_abi": { "exports": [ { "key": "geva::GEVACluster", "hash": "678d2f1241a5a5b0" }, { "key": "geva::GEVAGroupSet", "hash": "92c80dd11265a7c0" }, { "key": "geva::GEVAGroupedSummary", "hash": "4af4e62fd8199000" }, { "key": "geva::GEVAInput", "hash": "6c727552f4ed6a63" }, { "key": "geva::GEVAQuantiles", "hash": "52bb89e4a2b062a9" }, { "key": "geva::GEVAQuantilesAdjusted", "hash": "236d56b5288a1b6f" }, { "key": "geva::GEVAResults", "hash": "dd9cf1785b49e984" }, { "key": "geva::GEVASummary", "hash": "d344099f44e5ebe3" }, { "key": "geva::SVAttribute", "hash": "a37fbe24aed16154" }, { "key": "geva::SVChrAttribute", "hash": "06bda5ee1ef0c351" }, { "key": "geva::SVIntAttribute", "hash": "5b1300298c6887bd" }, { "key": "geva::SVNumAttribute", "hash": "82b6f47f95f844b6" }, { "key": "geva::SVTable", "hash": "01caee189c810d48" }, { "key": "geva::TypedList", "hash": "687d0cccc908e6da" }, { "key": "geva::generic:analysis.params", "hash": "03504344f91b7c84" }, { "key": "geva::generic:as.indexes", "hash": "466b2a0cb3a6e933" }, { "key": "geva::generic:centroids", "hash": "099c666b75cdc20c" }, { "key": "geva::generic:classification.table", "hash": "c4e01b90bc230461" }, { "key": "geva::generic:classification.table<-", "hash": "572dda56af167f4b" }, { "key": "geva::generic:cluster.method", "hash": "7371595f63074ec3" }, { "key": "geva::generic:elem.class", "hash": "2e78e84792b96548" }, { "key": "geva::generic:elem.class<-", "hash": "47379f0b633e96b5" }, { "key": "geva::generic:factors", "hash": "85d7a6670f3daba0" }, { "key": "geva::generic:factors<-", "hash": "b52487faaa7626a1" }, { "key": "geva::generic:featureTable", "hash": "138b9c3103b9e189" }, { "key": "geva::generic:featureTable<-", "hash": "8b264336e534913c" }, { "key": "geva::generic:group.rels", "hash": "6c3c6e9a6c1b0066" }, { "key": "geva::generic:groups", "hash": "98ccf98f3be3e570" }, { "key": "geva::generic:groupsets", "hash": "70d76ab782716e8d" }, { "key": "geva::generic:groupsets<-", "hash": "9ac64bc0aa9e0553" }, { "key": "geva::generic:infolist", "hash": "dae13d20bb8b2db4" }, { "key": "geva::generic:infolist<-", "hash": "89720ae9fe2c7086" }, { "key": "geva::generic:inputdata", "hash": "587f86582a0ed917" }, { "key": "geva::generic:inputnames", "hash": "132f7f078e2e5b92" }, { "key": "geva::generic:inputvalues", "hash": "3281be5dde57dc6d" }, { "key": "geva::generic:inputweights", "hash": "0b294430b7df5d75" }, { "key": "geva::generic:offsets", "hash": "df4e4fce98040e0d" }, { "key": "geva::generic:qareasizes", "hash": "f435b11bd827b536" }, { "key": "geva::generic:qcount", "hash": "03bc5296a7622c18" }, { "key": "geva::generic:qindexes", "hash": "58be2412bd4e68ca" }, { "key": "geva::generic:quantiles", "hash": "eb575119a50977ec" }, { "key": "geva::generic:quantiles.method", "hash": "0581fc3a5539351a" }, { "key": "geva::generic:results.table", "hash": "31054cba674eb1b8" }, { "key": "geva::generic:scores", "hash": "fc33b4ec184a24bc" }, { "key": "geva::generic:sv", "hash": "3d9915912c7fef23" }, { "key": "geva::generic:sv.data", "hash": "3a02f1d25ceda138" }, { "key": "geva::generic:sv.method", "hash": "a8f0b2dcac9a6881" }, { "key": "geva::generic:sv.scores", "hash": "f95e0bacd2ede038" }, { "key": "geva::generic:svattr", "hash": "0125ca544c8a837f" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/geva.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_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", "dimnames,SVTable-method", "format.SVTable", "head.SVTable", "is.na.SVTable", "length,SVTable-method", "names,SVTable-method", "plot,SVTable,missing-method", "points.SVTable", "show,SVTable-method", "summary.SVTable", "sv,SVTable-method", "sv.data,SVTable-method", "SVTable", "svtable", "SVTable-class", "tail.SVTable", "variation.SVTable", "with.SVTable", "[,SVTable,ANY,ANY,ANY-method" ] }, { "page": "top.genes", "title": "Top Results from GEVA", "topics": [ "top.genes" ] }, { "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", "elem.class<-,TypedList,character-method", "show,TypedList-method", "typed.list", "TypedList-class", "[,TypedList,ANY,missing,missing-method", "[<-,TypedList,character,missing-method" ] } ], "_readme": "https://github.com/bioc/geva/raw/HEAD/README.md", "_rundeps": [ "dbscan", "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 } ], "_score": 4, "_indexed": true, "_nocasepkg": "geva", "_universes": [ "bioc", "nunesijg", "sbcblab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-11-04T13:40:30.000Z", "distro": "resolute", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/ebe8ffc6a9a3911e312079ca2194b70fa1eadb44d55211a86d6dfa9dbe8eb569", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" }, { "r": "4.6.2", "os": "linux", "version": "1.21.0", "date": "2026-11-04T13:41:41.000Z", "distro": "resolute", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/e35bd789f923f6913d253bf6422949a7e3a69da733707c72f7b88ae3aeee07d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-11-04T13:39:32.000Z", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/dded488f3854b67ae8a851a4034ee61938176e86e26bd5cbbaa895cda3c4ec88", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" }, { "r": "4.6.2", "os": "mac", "version": "1.21.0", "date": "2026-11-04T13:39:27.000Z", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/b3ea30af731a7b27c6bccab46896ddb0df21964551cfb5ba629655140feb505f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-11-04T13:40:04.000Z", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/530019400fbf4372b100e0c4661f5ff3b636a9144bb8091cca48cd4e6086cbff", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-11-04T13:39:21.000Z", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/3516841bbcbd5c874cb858aa6b19e2501ed89c71312f11ea9bbb26fd09d1a617", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-11-04T13:39:25.000Z", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/1b5b2eddafa46109921024becdbbd5f92587e36a3259c1b96789fa1ffd6b2afd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" }, { "r": "4.6.2", "os": "win", "version": "1.21.0", "date": "2026-11-04T13:39:21.000Z", "commit": "bbc8940ea2412049e10ed6bbbc8e26c2d5cdd260", "fileid": "https://r2.ropensci.org/aa03c45267e86d2053432ff9625065dcd845c2e8427fa7a240c226c1f75f9311", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41839121227" } ] }