{ "_id": "6a1fe61fb401979e7343c415", "Package": "goSorensen", "Type": "Package", "Title": "Statistical inference based on the Sorensen-Dice dissimilarity\nand the Gene Ontology (GO)", "Version": "1.14.0", "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(\"Alexandre\", \"Sanchez-Pla\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-8673-7737\")),\nperson(\"Miquel\", \"Salicru\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9644-5626\")))", "VignetteBuilder": "knitr", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 08:17:07 UTC", "User": "root" }, "biocViews": "Annotation, GO, GeneSetEnrichment, Software, Microarray,\nPathways, GeneExpression, MultipleComparison, GraphAndNetwork,\nReactome, Clustering, KEGG", "Author": "Pablo Flores [aut, cre]\n(), Jordi Ocana [aut,\nctb] (0000-0002-4736-699), Alexandre Sanchez-Pla [ctb]\n(), Miquel Salicru [ctb]\n()", "Maintainer": "Pablo Flores ", "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-release.r-universe.dev", "Date/Publication": "2026-04-28 12:58:47 UTC", "RemoteUrl": "https://github.com/bioc/goSorensen", "RemoteRef": "RELEASE_3_23", "RemoteSha": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "MD5sum": "5f3487a4217f5f87b52f0e5f525b1687", "_user": "bioc-release", "_type": "src", "_file": "goSorensen_1.14.0.tar.gz", "_fileid": "16c98a0e4de57c993858079c5d81824ee57aad4760d38b110a36eed3fef2e38c", "_filesize": 765819, "_sha256": "16c98a0e4de57c993858079c5d81824ee57aad4760d38b110a36eed3fef2e38c", "_created": "2026-06-03T08:17:07.000Z", "_published": "2026-06-03T08:30:22.955Z", "_jobs": [ { "job": 79251129330, "time": 413, 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"description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 296, "source": "https://www.bioconductor.org/packages/stats/bioc/goSorensen" }, "_searchresults": 14, "_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": "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": false, "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": "allOncoGeneLists", "title": "7 gene lists possibly related with cancer", "object": "allOncoGeneLists", "file": "allOncoGeneLists.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "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_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_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": "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": 489, "table": true, "tojson": true }, { "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_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": "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": 3907, "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": "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": "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": "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": "Creates a 2x2 enrichment contingency table from two gene lists, or all pairwise contingency tables for a \"list\" of gene lists.", "topics": [ "buildEnrichTable", "buildEnrichTable.character", "buildEnrichTable.default", "buildEnrichTable.list" ] }, { "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_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_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 Sorensen-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.character", "enrichedIn.default", "enrichedIn.list" ] }, { "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_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_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", "equivTestSorensen.list", "equivTestSorensen.matrix", "equivTestSorensen.numeric", "equivTestSorensen.table", "equivTestSorensen.tableList" ] }, { "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 equivalence 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 class \"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/RELEASE_3_23/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", 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"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": "Jordi Ocaña, Pablo Flores", "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.", "For Two or More Lists.", "NOTE:", "ENRICHMENT CONTINGENCY TABLES", "For a Specific Ontology and one GO Level.", "Contingency Tables for Two Lists.", "Contingency Tables for Two or More Lists.", "For More than One Ontology and GO Level.", "EQUIVALENCE TESTS.", "For a Specific Ontology and GO level.", "Equivalence Test for Two Lists.", "Equivalence Test for Two or More Lists.", "For More than One Ontology and GO level.", "References" ], "created": "2022-06-16 21:12:09", "modified": "2024-12-11 23:11:16", "commits": 11 }, { "source": "Dissimilarities_Matrix.Rmd", "filename": "Dissimilarities_Matrix.html", "title": "Working with the Irrelevance-threshold Matrix of Dissimilarities.", "author": "Pablo Flores, Jordi Ocaña", "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 and one GO level.", "NOTE:", "For More than One Ontology and GO Level.", "Representing a Dissimilarity Matrix in Statistical Graphs.", "Dendrogram.", "MDS-Biplot.", "Characterizing MDS-Biplot Dimensions.", "Step 1. Split the biplot axis:", "Step 2. Obtain the matrix of GO terms enrichment:", "Step 3. Compute means and variances:", "Step 4. Establish a statistic:", "Step 5. Select the GO terms with the highest statistic:", "References" ], "created": "2024-11-30 20:14:00", "modified": "2025-03-18 23:02:55", "commits": 6 } ], "_score": 4.447158031342219, "_indexed": false, "_nocasepkg": "gosorensen", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/goSorensen", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.14.0", "date": "2026-06-03T08:24:49.000Z", "distro": "noble", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "308aa98e7e10f222f69fdbe4ecb878865b0c33f826f9dfa63197e600169080e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" }, { "r": "4.6.0", "os": "linux", "version": "1.14.0", "date": "2026-06-03T08:24:14.000Z", "distro": "noble", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "726f71805dd4fc0254bab364b4ec361f103ab6b7135fffb11cd33933c9df7173", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" }, { "r": "4.5.3", "os": "mac", "version": "1.14.0", "date": "2026-06-03T08:20:18.000Z", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "839e91e47a4e08a4502db53c6508036a038d5fcd29ab215ee671fb9aa0582a37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" }, { "r": "4.6.0", "os": "mac", "version": "1.14.0", "date": "2026-06-03T08:21:04.000Z", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "8be06084bd9a907608623142178ed6175f17ede175b5ac1067d7f921737277e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" }, { "r": "4.6.0", "os": "wasm", "version": "1.14.0", "date": "2026-06-03T08:24:10.000Z", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "df938451ab04b16764daa72c14b38ddcce55499b5c598c492a625652d0a7bc96", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" }, { "r": "4.7.0", "os": "win", "version": "1.14.0", "date": "2026-06-03T08:21:35.000Z", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "871b09982ec76f34c050d84cdd6353dd189f2d5983156b81c824f6422f0e195b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" }, { "r": "4.5.3", "os": "win", "version": "1.14.0", "date": "2026-06-03T08:21:02.000Z", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "e967f48a99b5650e365a487fb6184aee86ffc2887c773f245fb5b7e7a012db52", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" }, { "r": "4.6.0", "os": "win", "version": "1.14.0", "date": "2026-06-03T08:21:07.000Z", "commit": "04e9f1ec30660d4ba4531652be6ceeeb6c7a904f", "fileid": "f70878b8b013a184df149b14bc5aab428e95965ac1a676e7bf37837295243505", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26872053840" } ] }