{ "_id": "6aef1c57a2c425adab3298cf", "Package": "geNetClassifier", "Type": "Package", "Title": "Classify diseases and build associated gene networks using gene\nexpression profiles", "Version": "1.52.0", "Date": "2020-04-02", "Author": "Sara Aibar, Celia Fontanillo and Javier De Las Rivas.\nBioinformatics and Functional Genomics Group. Cancer Research\nCenter (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.", "Maintainer": "Sara Aibar ", "Description": "Comprehensive package to automatically train and validate\na multi-class SVM classifier based on gene expression data.\nProvides transparent selection of gene markers, their\ncoexpression networks, and an interface to query the\nclassifier.", "License": "GPL (>= 2)", "ZipData": "no", "URL": "http://www.cicancer.org", "LazyLoad": "yes", "Collate": "class.GenesRanking.R class.GenesNetwork.R\nclass.GeneralizationError.R class.GeNetClassifierReturn.R\nfunctions.private.R functions.public.R function.main.R", "biocViews": "Classification, DifferentialExpression, Microarray", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:37:36 UTC", "RemoteUrl": "https://github.com/bioc/geNetClassifier", "RemoteRef": "RELEASE_3_23", "RemoteSha": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-07 12:32:19 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "geNetClassifier_1.52.0.tar.gz", "_fileid": "https://r2.ropensci.org/f873f63fd043847538f90302713a0fdeda6b5aa34862197e0a26393dd2448ca9", "_filesize": 4087377, "_sha256": "f873f63fd043847538f90302713a0fdeda6b5aa34862197e0a26393dd2448ca9", "_expires": "2027-02-15T12:40:53.000Z", "_created": "2026-11-07T12:32:19.000Z", "_published": "2026-11-07T12:40:55.799Z", "_upstream": "https://github.com/bioc/geNetClassifier", "_status": "success", "_maintainer": { "name": "Sara Aibar", "email": "saibar@usal.es" }, "_jobs": [ { "job": 128404687112, "time": 116, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13573669295" }, { "job": 128404687160, "time": 195, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13573839059" }, { "job": 128404687180, "time": 222, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13574687647" }, { "job": 128404687177, "time": 152, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13574960337" }, { "job": 128404687189, "time": 143, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13573664764" }, { "job": 128403859210, "time": 223, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13573733971" }, { "job": 128404687201, "time": 79, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13574019093" }, { "job": 128404687221, "time": 96, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13574816306" }, { "job": 128404687253, "time": 137, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13574327274" }, { "job": 128404687146, "time": 105, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13573739147" } ], "_bioccheck": { "error": 2, "warning": 3, "note": 20 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821", "_commit": { "id": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379856 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10.1", "role": "Depends" }, { "package": "Biobase", "version": ">= 2.5.5", "role": "Depends" }, { "package": "EBarrays", "role": "Depends" }, { "package": "minet", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "e1071", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "leukemiasEset", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Enhances" }, { "package": "igraph", "role": "Enhances" }, { "package": "infotheo", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 2, "_updates": [ { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.53.0", "bioc": "3.24", "repository": "bioc", "r": "4.6.0" }, { "branch": "release", "version": "1.52.0", "bioc": "3.23", "repository": "bioc", "r": "4.6.0" } ], "_topics": [ "classification", "differentialexpression", "microarray" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 485, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 710, "source": "https://www.bioconductor.org/packages/stats/bioc/geNetClassifier" }, "_mentions": 2, "_searchresults": 1, "_abi": { "exports": [ { "key": "geNetClassifier::GeNetClassifierReturn", "hash": "3c4f52de63111514" }, { "key": "geNetClassifier::GeneralizationError", "hash": "57836a52562a5df0" }, { "key": "geNetClassifier::GenesNetwork", "hash": "0d4aaed499b482a0" }, { "key": "geNetClassifier::GenesRanking", "hash": "616a72f9382cc3fd" }, { "key": "geNetClassifier::generic:edges", "hash": "e17c52833c26e209" }, { "key": "geNetClassifier::generic:extractGenes", "hash": "7e3359633975638b" }, { "key": "geNetClassifier::generic:gClasses", "hash": "ca299078be17677d" }, { "key": "geNetClassifier::generic:gSlots", "hash": "d0a090b8e8e23983" }, { "key": "geNetClassifier::generic:genesDetails", "hash": "d95712c1674a0758" }, { "key": "geNetClassifier::generic:getEdges", "hash": "9f8a7a06cc5d650a" }, { "key": "geNetClassifier::generic:getNodes", "hash": "d8702ff418d2789d" }, { "key": "geNetClassifier::generic:getNumEdges", "hash": "1a62eb31a565e5bf" }, { "key": "geNetClassifier::generic:getNumNodes", "hash": "5c1959df2d8bf8c4" }, { "key": "geNetClassifier::generic:getRanking", "hash": "2f8b4b2dfe8ce41e" }, { "key": "geNetClassifier::generic:getSubNetwork", "hash": "284d815d18e78136" }, { "key": "geNetClassifier::generic:getTopRanking", "hash": "0b72656a172bec68" }, { "key": "geNetClassifier::generic:is.empty", "hash": "de9ed1a5ee4b9053" }, { "key": "geNetClassifier::generic:network2txt", "hash": "d25bdb5bd7974085" }, { "key": "geNetClassifier::generic:nodes", "hash": "b1eff371c34d6794" }, { "key": "geNetClassifier::generic:numEdges", "hash": "9ad2cbe13146c618" }, { "key": "geNetClassifier::generic:numGenes", "hash": "80d036076324e194" }, { "key": "geNetClassifier::generic:numNodes", "hash": "ae33fac98832e58f" }, { "key": "geNetClassifier::generic:numSignificantGenes", "hash": "307e1a51500361c0" }, { "key": "geNetClassifier::generic:overview", "hash": "fe9b8ddc0c3627cb" }, { "key": "geNetClassifier::generic:setProperties", "hash": "34b35c4cfbba1586" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/geNetClassifier.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calculateGenesRanking", "externalValidation.probMatrix", "externalValidation.stats", "gClasses", "genesDetails", "geNetClassifier", "getEdges", "getNodes", "getNumEdges", "getNumNodes", "getRanking", "getSubNetwork", "getTopRanking", "initialize", "network2txt", "numGenes", "numSignificantGenes", "overview", "plot.GenesNetwork", "plot.GenesRanking", "plot.GeNetClassifierReturn", "plotAssignments", "plotDiscriminantPower", "plotExpressionProfiles", "plotNetwork", "queryGeNetClassifier", "querySummary", "setProperties", "show" ], "_datasets": [ { "name": "geneSymbols", "title": "Gene symbols associated to human Ensemble IDs.", "object": "geneSymbols", "file": "geneSymbols.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "leukemiasClassifier", "title": "Sample leukemias classifier", "object": "leukemiasClassifier", "file": "leukemiasClassifier.RData", "class": [ "GeNetClassifierReturn" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "geNetClassifier-package", "title": "classify diseases and build associated gene networks using gene expression profiles", "topics": [ "geNetClassifier-package" ] }, { "page": "calculateGenesRanking", "title": "Calculate GenesRanking", "topics": [ "calculateGenesRanking" ] }, { "page": "externalValidation.probMatrix", "title": "Probability matrix.", "topics": [ "externalValidation.probMatrix" ] }, { "page": "externalValidation.stats", "title": "Statistics of the external validation.", "topics": [ "externalValidation.stats" ] }, { "page": "gClasses-methods", "title": "Classes in the ranking.", "topics": [ "gClasses", "gClasses,GenesRanking-method", "gClasses-methods" ] }, { "page": "GeneralizationError-class", "title": "Class \"GeneralizationError\" (slot of GeNetClassifierReturn)", "topics": [ "GeneralizationError", "GeneralizationError-class", "initialize,GeneralizationError-method", "show,GeneralizationError-method" ] }, { "page": "genesDetails-methods", "title": "Details of the genes in the network.", "topics": [ "genesDetails", "genesDetails,GenesRanking-method", "genesDetails-methods", "genesDetails.GenesRanking" ] }, { "page": "GenesNetwork-class", "title": "Class \"GenesNetwork\"", "topics": [ "GenesNetwork", "GenesNetwork-class", "initialize,GenesNetwork-method", "show,GenesNetwork-method" ] }, { "page": "GenesRanking-class", "title": "Class \"GenesRanking\"", "topics": [ "extractGenes,GenesRanking-method", "GenesRanking", "GenesRanking-class", "initialize,GenesRanking-method", "show,GenesRanking-method" ] }, { "page": "geneSymbols", "title": "Gene symbols associated to human Ensemble IDs.", "topics": [ "geneSymbols" ] }, { "page": "geNetClassifier", "title": "Main function of the geNetClassifier package. Trains the multi-class SVM classifier based on the given gene expression data through transparent detection of gene markers and their associated networks.", "topics": [ "geNetClassifier" ] }, { "page": "GeNetClassifierReturn-class", "title": "Class \"GeNetClassifierReturn\"", "topics": [ "GeNetClassifierReturn", "GeNetClassifierReturn-class", "getSlots,GeNetClassifierReturn-method", "initialize,GeNetClassifierReturn-method", "names,GeNetClassifierReturn-method", "show,GeNetClassifierReturn-method" ] }, { "page": "getEdges-methods", "title": "Edges in the network.", "topics": [ "edges,GenesNetwork-method", "getEdges", "getEdges,GenesNetwork-method", "getEdges-methods" ] }, { "page": "getNodes-methods", "title": "Nodes in the network.", "topics": [ "getNodes", "getNodes,GenesNetwork-method", "getNodes-methods", "nodes,GenesNetwork-method" ] }, { "page": "getNumEdges-methods", "title": "Number of edges in the network.", "topics": [ "getNumEdges", "getNumEdges,GenesNetwork-method", "getNumEdges-methods", "numEdges,GenesNetwork-method" ] }, { "page": "getNumNodes-methods", "title": "Number of nodes in the network.", "topics": [ "getNumNodes", "getNumNodes,GenesNetwork-method", "getNumNodes-methods", "numNodes,GenesNetwork-method" ] }, { "page": "getRanking-methods", "title": "Shows the genes ranking.", "topics": [ "getRanking", "getRanking,GenesRanking-method", "getRanking-methods", "getRanking.GenesRanking" ] }, { "page": "getSubNetwork-methods", "title": "Get a sub-network.", "topics": [ "getSubNetwork", "getSubNetwork,GenesNetwork-method", "getSubNetwork,GeNetClassifierReturn-method", "getSubNetwork,list-method", "getSubNetwork,NULL-method", "getSubNetwork-methods" ] }, { "page": "getTopRanking-methods", "title": "Gets a new ranking with the given top genes.", "topics": [ "getTopRanking", "getTopRanking,GenesRanking-method", "getTopRanking-methods", "getTopRanking.GenesRanking" ] }, { "page": "leukemiasClassifier", "title": "Sample leukemias classifier", "topics": [ "leukemiasClassifier" ] }, { "page": "network2txt", "title": "network2txt", "topics": [ "network2txt", "network2txt,GenesNetwork-method", "network2txt,list-method", "network2txt-methods" ] }, { "page": "numGenes-methods", "title": "Number of genes in the genesRanking.", "topics": [ "numGenes", "numGenes,GenesRanking-method", "numGenes-methods" ] }, { "page": "numSignificantGenes-methods", "title": "Number of ranked genes over the posterior probability threshold.", "topics": [ "numSignificantGenes", "numSignificantGenes,GenesRanking-method", "numSignificantGenes-methods", "numSignificantGenes.GenesRanking" ] }, { "page": "overview-methods", "title": "Overview", "topics": [ "overview", "overview,GeneralizationError-method", "overview,GenesNetwork-method", "overview,GenesRanking-method", "overview,GeNetClassifierReturn-method", "overview-methods" ] }, { "page": "plot.GenesRanking", "title": "Plot GenesRanking", "topics": [ "plot,GenesRanking-method", "plot.GenesRanking", "plotGenesRanking" ] }, { "page": "plot.GeNetClassifierReturn", "title": "Plot GeNetClassifierReturn", "topics": [ "plot,GeNetClassifierReturn-method", "plot.GeNetClassifierReturn", "plotGeNetClassifierReturn", "plotGeNetClassifierReturn,GeNetClassifierReturn-method" ] }, { "page": "plotAssignments", "title": "Plot assignment probabilities", "topics": [ "plotAssignments" ] }, { "page": "plotDiscriminantPower", "title": "Plots the genes' Discriminant Power.", "topics": [ "plotDiscriminantPower" ] }, { "page": "plotExpressionProfiles", "title": "Expression profiles plot.", "topics": [ "plotExpressionProfiles" ] }, { "page": "plotNetwork", "title": "Plot GenesNetwork", "topics": [ "plot,GenesNetwork-method", "plot.GenesNetwork", "plotNetwork", "plotNetwork,GenesNetwork-method" ] }, { "page": "queryGeNetClassifier", "title": "Queries the classifier trained with geNetClassifier.", "topics": [ "queryGeNetClassifier" ] }, { "page": "querySummary", "title": "Summary of the query.", "topics": [ "querySummary" ] }, { "page": "setProperties-methods", "title": "Set properties", "topics": [ "setProperties", "setProperties,GenesRanking-method", "setProperties-methods", "setProperties.GenesRanking" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "class", "cluster", "e1071", "EBarrays", "generics", "infotheo", "lattice", "minet", "proxy" ], "_vignettes": [ { "source": "geNetClassifier-vignette.Rnw", "filename": "geNetClassifier-vignette.pdf", "title": "geNetClassifier-vignette", "engine": "utils::Sweave", "headings": [ "Introduction to geNetClassifier", "Install the package and example data", "Main function of the package: geNetClassifier() ", "External validation: query with new samples of known class", "Sample classification: query with new samples of unknown class", "Functions to plot the results" ], "created": "2013-03-29 21:14:40", "modified": "2018-08-30 17:49:23", "commits": 9 } ], "_score": 4.079181246047625, "_indexed": false, "_nocasepkg": "genetclassifier", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/geNetClassifier", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.52.0", "date": "2026-11-07T12:34:58.000Z", "distro": "resolute", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/8b156790bd89ac15e6f6a4c51a3f2a1a74489f357319214eea2d0eb96cdeb7cd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" }, { "r": "4.6.2", "os": "linux", "version": "1.52.0", "date": "2026-11-07T12:35:36.000Z", "distro": "resolute", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/d46e814503bb1dec086799e56badcc5b8751194d81c202488ab8fb9ffc6c3722", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" }, { "r": "4.5.3", "os": "mac", "version": "1.52.0", "date": "2026-11-07T12:38:57.000Z", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/6a07d0abe329f7fb6d9cfa97765ba578a85331327fe12cb7b31e15365759bb4b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" }, { "r": "4.6.2", "os": "mac", "version": "1.52.0", "date": "2026-11-07T12:39:42.000Z", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/2e22b2b848d91548d6fa8dc42a58820e108940900e21386d519695ca5a33f250", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" }, { "r": "4.6.0", "os": "wasm", "version": "1.52.0", "date": "2026-11-07T12:34:05.000Z", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/5ce9fadfa77452a1b52e06b4b1e8df0f05e6474577a0e70b6c4ecdb116c67007", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" }, { "r": "4.7.0", "os": "win", "version": "1.52.0", "date": "2026-11-07T12:33:28.000Z", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/dd20a2dd1b4520b5caa7c3d03105dade5e494364ccb190ed55a052c1f06f1759", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" }, { "r": "4.5.3", "os": "win", "version": "1.52.0", "date": "2026-11-07T12:33:40.000Z", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/244958660c09a0d3caae0cc205afe62cd46956dfada0e7c7360dc7b67af8f5e7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" }, { "r": "4.6.2", "os": "win", "version": "1.52.0", "date": "2026-11-07T12:33:31.000Z", "commit": "59ec64e3abdc4a0f2ca2847a9458b5b80b2b9d3d", "fileid": "https://r2.ropensci.org/dc5b491ca28f077e3f0844c6af073329e475d89b398e6ae33719f5f05196f842", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42372662821" } ] }