{ "_id": "6a1983b5acfb0bcc41dfa7ed", "Package": "goSorensen", "Type": "Package", "Title": "Statistical inference based on the Sorensen-Dice dissimilarity\nand the Gene Ontology (GO)", "Version": "1.15.0", "Description": "This package implements inferential methods to compare\ngene lists in terms of their biological meaning as expressed in\nthe GO. The compared gene lists are characterized by\ncross-tabulation frequency tables of enriched GO items.\nDissimilarity between gene lists is evaluated using the\nSorensen-Dice index. The fundamental guiding principle is that\ntwo gene lists are taken as similar if they share a great\nproportion of common enriched GO items.", "Authors@R": "c(person(\"Pablo\", \"Flores\", role = c(\"aut\", \"cre\"),\nemail = \"p_flores@espoch.edu.ec\",\ncomment = c(ORCID = \"0000-0002-7156-8547\")),\nperson(\"Jordi\", \"Ocana\", role = c(\"aut\", \"ctb\"),\ncomment = c(ORCID = \"0000-0002-4736-6996\")),\nperson(\"Alex\", \"Mantilla\", role = c(\"aut\", \"ctb\"),\ncomment = c(ORCID = \"0000-0001-7047-7072\")),\nperson(\"Alexandre\", \"Sanchez-Pla\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-8673-7737\")),\nperson(\"Miquel\", \"Salicru\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9644-5626\")))", "URL": "https://github.com/pablof1988/goSorensen", "BugReports": "https://github.com/pablof1988/goSorensen/issues", "VignetteBuilder": "knitr", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "NeedsCompilation": "no", "biocViews": "Annotation, GO, GeneSetEnrichment, Software, Microarray,\nPathways, GeneExpression, MultipleComparison, GraphAndNetwork,\nReactome, Clustering, KEGG", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-12 21:09:13 UTC", "RemoteUrl": "https://github.com/bioc/goSorensen", "RemoteRef": "HEAD", "RemoteSha": "2d4ad98447cd238334a353098acc80e2720f5043", "Packaged": { "Date": "2026-05-29 10:48:53 UTC", "User": "root" }, "Author": "Pablo Flores [aut, cre] (ORCID:\n),\nJordi Ocana [aut, ctb] (ORCID: ),\nAlex Mantilla [aut, ctb] (ORCID:\n),\nAlexandre Sanchez-Pla [ctb] (ORCID:\n),\nMiquel Salicru [ctb] (ORCID: )", "Maintainer": "Pablo Flores ", "MD5sum": "4ba92aa3ab3e3316324c24473f24e20f", "_user": "bioc", "_type": "src", "_file": "goSorensen_1.15.0.tar.gz", "_fileid": "73614d4fd59baab83147dc58db17dd264ae0f946d925966da5c8b884447571bb", "_filesize": 882971, "_sha256": "73614d4fd59baab83147dc58db17dd264ae0f946d925966da5c8b884447571bb", "_created": "2026-05-29T10:48:53.000Z", "_published": "2026-05-29T12:16:53.836Z", "_jobs": [ { "job": 78486258209, "time": 408, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7289040161" }, { "job": 78486258214, "time": 557, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7289081527" }, { "job": 78486258261, "time": 529, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7289073748" }, { "job": 78486258205, "time": 230, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7290395290" }, { "job": 78486258195, "time": 323, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7290424597" }, { "job": 78484801561, "time": 632, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288924973" }, { "job": 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"branch": "devel", "version": "1.15.0", "bioc": "3.24" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23" } ], "_topics": [ "annotation", "go", "genesetenrichment", "software", "microarray", "pathways", "geneexpression", "multiplecomparison", "graphandnetwork", "reactome", "clustering", "kegg" ], "_stars": 2, "_contributors": [ { "user": "pablof1988", "count": 81, "uuid": 64914241 }, { "user": "jordiocana", "count": 34, "uuid": 20562509 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 300, "source": "https://www.bioconductor.org/packages/stats/bioc/goSorensen" }, "_devurl": "https://github.com/pablof1988/gosorensen", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/goSorensen.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "allBuildEnrichTable", "allEquivTestSorensen", "allHclustThreshold", "allSorenThreshold", "buildEnrichTable", "dSorensen", "duppSorensen", "enrichedIn", "equivTestSorensen", "getDissimilarity", "getEffNboot", "getNboot", "getPvalue", "getSE", "getTable", "getUpper", "hclustThreshold", "nice2x2Table", "pruneClusts", "seSorensen", "sorenThreshold", "upgrade" ], "_datasets": [ { "name": "allContTabs", "title": "Example of the output produced by the function 'allBuildEnrichTable'.", "object": "allContTabs", "file": "allContTabs.rda", "class": [ "allTableList", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "allContTabsNoLevel", "title": "Example of the output produced by the function 'allBuildEnrichTable'.", "object": "allContTabsNoLevel", "file": "allContTabsNoLevel.rda", "class": [ "allTableList", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "allDissMatrx", "title": "Example of the output produced by the function 'allSorenThreshold'. It contains the dissimilarity matrices for GO levels from 3 to 10 across the ontologies BP, CC and MF.", "object": "allDissMatrx", "file": "allDissMatrx.rda", "class": [ "distList", "list" ], "fields": [], "table": true, "tojson": false }, { "name": "allDissMatrxNoLevel", "title": "Example of the output produced by the function 'allSorenThreshold'. It contains the dissimilarity matrices without GO-Level restriction across the ontologies BP, CC and MF.", "object": "allDissMatrxNoLevel", "file": "allDissMatrxNoLevel.rda", "class": [ "distList", "list" ], "fields": [], "table": true, "tojson": false }, { "name": "allEqTests", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the normal asymptotic distribution.", "object": "allEqTests", "file": "allEqTests.rda", "class": [ "AllEquivSDhtest", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "allEqTests_boot", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the approximated bootstrap distribution.", "object": "allEqTests_boot", "file": "allEqTests_boot.rda", "class": [ "AllEquivSDhtest", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "allEqTests_bootNoLevel", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the approximated bootstrap distribution.", "object": "allEqTests_bootNoLevel", "file": "allEqTests_bootNoLevel.rda", "class": [ "AllEquivSDhtest", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "allEqTestsNoLevel", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the normal asymptotic distribution.", "object": "allEqTestsNoLevel", "file": "allEqTestsNoLevel.rda", "class": [ "AllEquivSDhtest", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "allOncoGeneLists", "title": "7 gene lists possibly related with cancer", "object": "allOncoGeneLists", "file": "allOncoGeneLists.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "cont_all_BP", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency tables for all the lists from 'allOncoGeneLists' for ontology BP without GO-Level restriction.", "object": "cont_all_BP", "file": "cont_all_BP.rda", "class": [ "tableList", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "cont_all_BP4", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency tables for all the lists from 'allOncoGeneLists' at level 4 of ontology BP.", "object": "cont_all_BP4", "file": "cont_all_BP4.rda", "class": [ "tableList", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "cont_atlas.sanger_BP", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency table for two lists for ontology BP without GO-Level restriction.", "object": "cont_atlas.sanger_BP", "file": "cont_atlas.sanger_BP.rda", "class": [ "table" ], "fields": [ "TRUE", "FALSE" ], "rows": 2, "table": true, "tojson": false }, { "name": "cont_atlas.sanger_BP4", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency table for two lists at level 4 of ontology BP.", "object": "cont_atlas.sanger_BP4", "file": "cont_atlas.sanger_BP4.rda", "class": [ "table" ], "fields": [ "TRUE", "FALSE" ], "rows": 2, "table": true, "tojson": false }, { "name": "dissMatrx_BP", "title": "Example of the output produced by the function 'sorenThreshold'. It contains the dissimilarity matrix for the ontology BP without GO-Level restriction.", "object": "dissMatrx_BP", "file": "dissMatrx_BP.rda", "class": [ "dist" ], "fields": [], "table": false, "tojson": false }, { "name": "dissMatrx_BP4", "title": "Example of the output produced by the function 'sorenThreshold'. It contains the dissimilarity matrix at GO level 4, for the ontology BP.", "object": "dissMatrx_BP4", "file": "dissMatrx_BP4.rda", "class": [ "dist" ], "fields": [], "table": false, "tojson": false }, { "name": "enrichedInBP", "title": "Example of the output produced by the function 'enrichedIn'. It contains exclusively GO terms enriched in at least one list of 'allOncoGeneLists', ontology BP, without GO-Level restriction.", "object": "enrichedInBP", "file": "enrichedInBP.rda", "class": [ "matrix", "array" ], "fields": [ "atlas", "cangenes", "cis", "miscellaneous", "sanger", "Vogelstein", "waldman" ], "rows": 2695, "table": true, "tojson": true }, { "name": "enrichedInBP4", "title": "Example of the output produced by the function 'enrichedIn'. It contains exclusively GO terms enriched in at least one list of 'allOncoGeneLists', ontology BP, GO-Level 4.", "object": "enrichedInBP4", "file": "enrichedInBP4.rda", "class": [ "matrix", "array" ], "fields": [ "atlas", "cangenes", "cis", "miscellaneous", "sanger", "Vogelstein", "waldman" ], "rows": 346, "table": true, "tojson": true }, { "name": "eqTest_all_BP", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains all the possible equivalence tests for the lists from 'allOncoGeneLists' in ontology BP without GO-Level restriction.", "object": "eqTest_all_BP", "file": "eqTest_all_BP.rda", "class": [ "equivSDhtestList", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "eqTest_all_BP4", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains all the possible equivalence tests for the lists from 'allOncoGeneLists' at level 4 of ontology BP.", "object": "eqTest_all_BP4", "file": "eqTest_all_BP4.rda", "class": [ "equivSDhtestList", "list" ], "fields": [], "table": false, "tojson": false }, { "name": "eqTest_atlas.sanger_BP", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains the equivalence test for comparing two lists in ontology BP without GO-Level restriction.", "object": "eqTest_atlas.sanger_BP", "file": "eqTest_atlas.sanger_BP.rda", "class": [ "equivSDhtest", "htest" ], "fields": [], "table": false, "tojson": false }, { "name": "eqTest_atlas.sanger_BP4", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains the equivalence test for comparing two lists at level 4 of ontology BP.", "object": "eqTest_atlas.sanger_BP4", "file": "eqTest_atlas.sanger_BP4.rda", "class": [ "equivSDhtest", "htest" ], "fields": [], "table": false, "tojson": false }, { "name": "fullEnrichedInBP", "title": "Example of the output produced by the function 'enrichedIn'. It contains all the GO terms enriched or not-enriched in the lists of 'allOncoGeneLists', ontology BP, without GO-Level restriction.", "object": "fullEnrichedInBP", "file": "fullEnrichedInBP.rda", "class": [ "matrix", "array" ], "fields": [ "atlas", "cangenes", "cis", "miscellaneous", "sanger", "Vogelstein", "waldman" ], "rows": 5880, "table": true, "tojson": true }, { "name": "fullEnrichedInBP4", "title": "Example of the output produced by the function 'enrichedIn'. It contains all the GO terms enriched or not-enriched in the lists of 'allOncoGeneLists', ontology BP, GO-Level 4.", "object": "fullEnrichedInBP4", "file": "fullEnrichedInBP4.rda", "class": [ "matrix", "array" ], "fields": [ "atlas", "cangenes", "cis", "miscellaneous", "sanger", "Vogelstein", "waldman" ], "rows": 3323, "table": true, "tojson": true }, { "name": "pbtGeneLists", "title": "14 gene lists possibly related with kidney transplant rejection", "object": "pbtGeneLists", "file": "pbtGeneLists.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "allBuildEnrichTable", "title": "Iterate 'buildEnrichTable' along the specified GO ontologies and GO levels", "topics": [ "allBuildEnrichTable" ] }, { "page": "allContTabs", "title": "Example of the output produced by the function 'allBuildEnrichTable'.", "topics": [ "allContTabs" ] }, { "page": "allContTabsNoLevel", "title": "Example of the output produced by the function 'allBuildEnrichTable'.", "topics": [ "allContTabsNoLevel" ] }, { "page": "allDissMatrx", "title": "Example of the output produced by the function 'allSorenThreshold'. It contains the dissimilarity matrices for GO levels from 3 to 10 across the ontologies BP, CC and MF.", "topics": [ "allDissMatrx" ] }, { "page": "allDissMatrxNoLevel", "title": "Example of the output produced by the function 'allSorenThreshold'. It contains the dissimilarity matrices without GO-Level restriction across the ontologies BP, CC and MF.", "topics": [ "allDissMatrxNoLevel" ] }, { "page": "allEqTests", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the normal asymptotic distribution.", "topics": [ "allEqTests" ] }, { "page": "allEqTests_boot", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the approximated bootstrap distribution.", "topics": [ "allEqTests_boot" ] }, { "page": "allEqTests_bootNoLevel", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the approximated bootstrap distribution.", "topics": [ "allEqTests_bootNoLevel" ] }, { "page": "allEqTestsNoLevel", "title": "Example of the output produced by the function 'allEquivTestSorensen' using the normal asymptotic distribution.", "topics": [ "allEqTestsNoLevel" ] }, { "page": "allEquivTestSorensen", "title": "Iterate 'equivTestSorensen' along the specified GO ontologies and GO levels", "topics": [ "allEquivTestSorensen", "allEquivTestSorensen.allTableList", "allEquivTestSorensen.list" ] }, { "page": "allHclustThreshold", "title": "Iterate 'hclustThreshold' along the specified GO ontologies and GO levels", "topics": [ "allHclustThreshold" ] }, { "page": "allOncoGeneLists", "title": "7 gene lists possibly related with cancer", "topics": [ "allOncoGeneLists" ] }, { "page": "allSorenThreshold", "title": "Iterate 'sorenThreshold' along the specified GO ontologies and GO levels", "topics": [ "allSorenThreshold", "allSorenThreshold.allTableList", "allSorenThreshold.list" ] }, { "page": "boot.tStat", "title": "Studentized Sorensen-Dice dissimilarity statistic", "topics": [ "boot.tStat" ] }, { "page": "buildEnrichTable", "title": "Create enrichment contingency tables from gene lists", "topics": [ "buildEnrichTable", "buildEnrichTable.default", "buildEnrichTable.list" ] }, { "page": "cont_all_BP", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency tables for all the lists from 'allOncoGeneLists' for ontology BP without GO-Level restriction.", "topics": [ "cont_all_BP" ] }, { "page": "cont_all_BP4", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency tables for all the lists from 'allOncoGeneLists' at level 4 of ontology BP.", "topics": [ "cont_all_BP4" ] }, { "page": "cont_atlas.sanger_BP", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency table for two lists for ontology BP without GO-Level restriction.", "topics": [ "cont_atlas.sanger_BP" ] }, { "page": "cont_atlas.sanger_BP4", "title": "Example of the output produced by the function 'buildEnrichTable'. It contains the enrichment contingency table for two lists at level 4 of ontology BP.", "topics": [ "cont_atlas.sanger_BP4" ] }, { "page": "dissMatrx_BP", "title": "Example of the output produced by the function 'sorenThreshold'. It contains the dissimilarity matrix for the ontology BP without GO-Level restriction.", "topics": [ "dissMatrx_BP" ] }, { "page": "dissMatrx_BP4", "title": "Example of the output produced by the function 'sorenThreshold'. It contains the dissimilarity matrix at GO level 4, for the ontology BP.", "topics": [ "dissMatrx_BP4" ] }, { "page": "dSorensen", "title": "Computation of the Sorensen-Dice dissimilarity", "topics": [ "dSorensen", "dSorensen.character", "dSorensen.list", "dSorensen.matrix", "dSorensen.numeric", "dSorensen.table", "dSorensen.tableList" ] }, { "page": "duppSorensen", "title": "Upper limit of a one-sided confidence interval (0, dUpp] for the S orensen-Dice dissimilarity", "topics": [ "duppSorensen", "duppSorensen.character", "duppSorensen.list", "duppSorensen.matrix", "duppSorensen.numeric", "duppSorensen.table", "duppSorensen.tableList" ] }, { "page": "enrichedIn", "title": "This function builds a cross-tabulation of enriched (TRUE) and non-enriched (FALSE) GO terms vs. gene lists", "topics": [ "enrichedIn", "enrichedIn.default" ] }, { "page": "enrichedInBP", "title": "Example of the output produced by the function 'enrichedIn'. It contains exclusively GO terms enriched in at least one list of 'allOncoGeneLists', ontology BP, without GO-Level restriction.", "topics": [ "enrichedInBP" ] }, { "page": "enrichedInBP4", "title": "Example of the output produced by the function 'enrichedIn'. It contains exclusively GO terms enriched in at least one list of 'allOncoGeneLists', ontology BP, GO-Level 4.", "topics": [ "enrichedInBP4" ] }, { "page": "eqTest_all_BP", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains all the possible equivalence tests for the lists from 'allOncoGeneLists' in ontology BP without GO-Level restriction.", "topics": [ "eqTest_all_BP" ] }, { "page": "eqTest_all_BP4", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains all the possible equivalence tests for the lists from 'allOncoGeneLists' at level 4 of ontology BP.", "topics": [ "eqTest_all_BP4" ] }, { "page": "eqTest_atlas.sanger_BP", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains the equivalence test for comparing two lists in ontology BP without GO-Level restriction.", "topics": [ "eqTest_atlas.sanger_BP" ] }, { "page": "eqTest_atlas.sanger_BP4", "title": "Example of the output produced by the function 'equivTestSorensen'. It contains the equivalence test for comparing two lists at level 4 of ontology BP.", "topics": [ "eqTest_atlas.sanger_BP4" ] }, { "page": "equivTestSorensen", "title": "Equivalence test based on the Sorensen-Dice dissimilarity", "topics": [ "equivTestSorensen", "equivTestSorensen.character" ] }, { "page": "fullEnrichedInBP", "title": "Example of the output produced by the function 'enrichedIn'. It contains all the GO terms enriched or not-enriched in the lists of 'allOncoGeneLists', ontology BP, without GO-Level restriction.", "topics": [ "fullEnrichedInBP" ] }, { "page": "fullEnrichedInBP4", "title": "Example of the output produced by the function 'enrichedIn'. It contains all the GO terms enriched or not-enriched in the lists of 'allOncoGeneLists', ontology BP, GO-Level 4.", "topics": [ "fullEnrichedInBP4" ] }, { "page": "getDissimilarity", "title": "Access to the estimated Sorensen-Dice dissimilarity in one or more e quivalence test results", "topics": [ "getDissimilarity", "getDissimilarity.AllEquivSDhtest", "getDissimilarity.equivSDhtest", "getDissimilarity.equivSDhtestList" ] }, { "page": "getEffNboot", "title": "Access to the number of effective bootstrap replicates in one or more equivalence test results (only for their bootstrap version)", "topics": [ "getEffNboot", "getEffNboot.AllEquivSDhtest", "getEffNboot.equivSDhtest", "getEffNboot.equivSDhtestList" ] }, { "page": "getNboot", "title": "Access to the number of initially planned bootstrap replicates in one or more equivalence test results (only in their bootstrap version)", "topics": [ "getNboot", "getNboot.AllEquivSDhtest", "getNboot.equivSDhtest", "getNboot.equivSDhtestList" ] }, { "page": "getPvalue", "title": "Access to the p-value of one or more equivalence test results", "topics": [ "getPvalue", "getPvalue.AllEquivSDhtest", "getPvalue.equivSDhtest", "getPvalue.equivSDhtestList" ] }, { "page": "getSE", "title": "Access to the estimated standard error of the sample Sorensen-Dice dissimilarity in one or more equivalence test results", "topics": [ "getSE", "getSE.AllEquivSDhtest", "getSE.equivSDhtest", "getSE.equivSDhtestList" ] }, { "page": "getTable", "title": "Access to the contingency table of mutual enrichment of one or more equivalence test results", "topics": [ "getTable", "getTable.AllEquivSDhtest", "getTable.equivSDhtest", "getTable.equivSDhtestList" ] }, { "page": "getUpper", "title": "Access to the upper limit of the one-sided confidence intervals for the Sorensen-Dice dissimilarity in one or more equivalence test results", "topics": [ "getUpper", "getUpper.AllEquivSDhtest", "getUpper.equivSDhtest", "getUpper.equivSDhtestList" ] }, { "page": "gosorensen", "title": "gosorensen: A package for making inference on gene lists based on the Sorensen-Dice dissimilarity", "topics": [ "goSorensen-package", "goSorensen", "gosorensen" ] }, { "page": "hclustThreshold", "title": "From a Sorensen-Dice threshold dissimilarity matrix, generate an object of c lass \"hclust\"", "topics": [ "hclustThreshold" ] }, { "page": "nice2x2Table", "title": "Checks for validity data representing an enrichment contingency table generated from two gene lists", "topics": [ "nice2x2Table", "nice2x2Table.matrix", "nice2x2Table.numeric", "nice2x2Table.table" ] }, { "page": "pbtGeneLists", "title": "14 gene lists possibly related with kidney transplant rejection", "topics": [ "pbtGeneLists" ] }, { "page": "pruneClusts", "title": "Remove all NULL or unrepresentable as a dendrogram \"equivClustSorensen\" elements in an object of class \"equivClustSorensenList\"", "topics": [ "pruneClusts" ] }, { "page": "seSorensen", "title": "Standard error of the sample Sorensen-Dice dissimilarity, asymptotic approach", "topics": [ "seSorensen", "seSorensen.character", "seSorensen.list", "seSorensen.matrix", "seSorensen.numeric", "seSorensen.table", "seSorensen.tableList" ] }, { "page": "sorenThreshold", "title": "For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold dissimilarity matrix.", "topics": [ "sorenThreshold", "sorenThreshold.list", "sorenThreshold.tableList" ] }, { "page": "upgrade", "title": "Update the result of a Sorensen-Dice equivalence test.", "topics": [ "upgrade", "upgrade.AllEquivSDhtest", "upgrade.equivSDhtest", "upgrade.equivSDhtestList" ] } ], "_readme": "https://github.com/bioc/goSorensen/raw/HEAD/README.md", "_rundeps": [ "aisdk", "AnnotationDbi", "ape", "aplot", "askpass", "base64enc", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "callr", "cli", "cluster", "clusterProfiler", "CompQuadForm", "cpp11", "crayon", "curl", "DBI", "digest", "DOSE", "dplyr", "enrichit", "enrichplot", "evaluate", "farver", "fastmap", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "gdtools", "generics", "ggforce", "ggfun", "ggiraph", "ggnewscale", "ggplot2", "ggplotify", "ggrepel", "ggtangle", "ggtree", "glue", "GO.db", "goProfiles", "GOSemSim", "gridGraphics", "gson", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "IRanges", "isoband", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mime", "nlme", "openssl", "patchwork", "pillar", "pkgconfig", "plyr", "png", "polyclip", "processx", "ps", "purrr", "qvalue", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "rmarkdown", "RSQLite", "S4Vectors", "S7", "sass", "scales", "scatterpie", "Seqinfo", "stringi", "stringr", "sys", "systemfonts", "tibble", "tidydr", "tidyr", "tidyselect", "tidytree", "tinytex", "treeio", "tweenr", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XVector", "yaml", "yulab.utils" ], "_vignettes": [ { "source": "goSorensen_Introduction.Rmd", "filename": "goSorensen_Introduction.html", "title": "An Introduction to goSorensen R-Package", "author": "Pablo Flores, Jordi Ocaña, Alex Mantilla", "engine": "knitr::rmarkdown", "headings": [ "PRELIMINARIES.", "Theoretical Framework of Reference.", "goSorensen Installation.", "Data Used in this Vignette.", "Before Using goSorensen.", "MATRIX OF GO TERMS ENRICHMENT.", "For One List (With or Without GO Level Restriction).", "For Two or More Lists (With or Without GO Level Restriction).", "NOTE:", "ENRICHMENT CONTINGENCY TABLES", "For a Specific Ontology (With or Without GO Level Restriction).", "Contingency Tables for Two Lists.", "Contingency Tables for Two or More Lists.", "For More than One Ontology and GO Configurations (Levels or No Level Restriction).", "EQUIVALENCE TESTS.", "Equivalence Test for Two Lists.", "Equivalence Test for Two or More Lists.", "For Multiple Ontologies and GO Configurations.", "References" ], "created": "2022-06-16 21:12:09", "modified": "2026-05-12 21:09:13", "commits": 12 }, { "source": "Dissimilarities_Matrix.Rmd", "filename": "Dissimilarities_Matrix.html", "title": "Working with the Irrelevance-threshold Matrix of Dissimilarities.", "author": "Pablo Flores, Jordi Ocaña, Alex Mantilla", "engine": "knitr::rmarkdown", "headings": [ "PRELIMINARIES.", "Theoretical Framework of Reference", "Data Used in this Vignette.", "Obtaining the Irrelevance-threshold Matrix of Dissimilarities.", "For a Specific Ontology, with or without GO level restriction.", "NOTE:", "For More than One Ontology, with or without GO level restriction.", "Representing a Dissimilarity Matrix in Statistical Graphs.", "Dendrogram.", "MDS-Biplot.", "Characterizing MDS-Biplot Dimensions.", "Step 1. 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