{ "_id": "6ac8a3aede46216d5edd4efe", "Package": "goProfiles", "Version": "1.75.0", "Title": "goProfiles: an R package for the statistical analysis of\nfunctional profiles", "Author": "Alex Sanchez, Jordi Ocana and Miquel Salicru", "Type": "Package", "Date": "2018-04-20", "Maintainer": "Alex Sanchez ", "Description": "The package implements methods to compare lists of genes\nbased on comparing the corresponding 'functional profiles'.", "License": "GPL-2", "biocViews": "Annotation, GO, GeneExpression, GeneSetEnrichment,\nGraphAndNetwork, Microarray, MultipleComparison, Pathways,\nSoftware", "url": "https://github.com/alexsanchezpla/goProfiles/wiki", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-09 08:14:11 UTC", "User": "root" }, "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:32:52 UTC", "RemoteUrl": "https://github.com/bioc/goProfiles", "RemoteRef": "HEAD", "RemoteSha": "8569caa971224ac79c322f7c854486847c011645", "_user": "bioc", "_type": "src", "_file": "goProfiles_1.75.0.tar.gz", "_fileid": "https://r2.ropensci.org/514a709167205a14f483479686eda62a86642f5dbf21a8452c3cd7094669b001", "_filesize": 531497, "_sha256": "514a709167205a14f483479686eda62a86642f5dbf21a8452c3cd7094669b001", "_expires": "2027-01-17T08:19:55.000Z", "_created": "2026-10-09T08:14:11.000Z", "_published": "2026-10-09T08:19:58.132Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37903321045", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 2, "warning": 8, "note": 17 }, "_upstream": "https://github.com/bioc/goProfiles", "_commit": { "id": "8569caa971224ac79c322f7c854486847c011645", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379572 }, "_maintainer": { "name": "Alex Sanchez", "email": "asanchez@ub.edu", "login": 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"bioc" } ], "_topics": [ "annotation", "go", "geneexpression", "genesetenrichment", "graphandnetwork", "microarray", "multiplecomparison", "pathways", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 474, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 677, "source": "https://www.bioconductor.org/packages/stats/bioc/goProfiles" }, "_mentions": 10, "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/goProfiles.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "as.GOTerms.frame", "as.GOTerms.list", "basicProfile", "BioCpack2EntrezIDS", "BioCpack2Profiles", "BioCprobes2Entrez", "compareGeneLists", "compareGOProfiles", "compareProfilesLists", "compSummary", "contractedProfile", "equivalentGOProfiles", "equivClust", "equivClust2pdf", "equivSummary", "expandedLevel", "expandedProfile", "expandTerm", "fisherGOProfiles", "fitGOProfile", "getAncestorsLst", "getGOLevel", "GOTermsFrame2GOTermsList", "GOTermsList", "iterEquivClust", "mergeProfilesLists", "ngenes", "plotProfiles", "printProfiles" ], "_datasets": [ { "name": "CD4LLids", "title": "Entrez identifiers for CD4-TCells example", "object": "CD4Ids", "file": "CD4Ids.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "clustKidneyMF2", "title": "Ready 2 cluster equivalence distance matrix obtained from the analysis of the \"Kidney Dataset\" at level 2 of the MF ontology", "object": "clustKidneyMF2", "file": "clustKidneyMF2.rda", "class": [ "equivClust", "hclust" ], "fields": [], "table": false, "tojson": false }, { "name": "diseaseIds", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "dominantIds", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "dominantIdsEBI", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "dominantIdsNCBI", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "drosophilaIds", "title": "Entrez identifiers for genes related with an eye mutation in drosophila", "object": "drosophila", "file": "drosophila.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "hugoIds", "title": "Entrez Identifiers obtained from the Human Genome Organization", "object": "hugoIds", "file": "hugoIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "kidneyGeneLists", "title": "Gene-lists related to kidney transplantation rejection", "object": "kidneyGeneLists", "file": "kidneyGeneLists.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "michaudIds", "title": "Entrez identifiers for genes related with an eye mutation in drosophila", "object": "drosophila", "file": "drosophila.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "morbidmapIds", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "ostrinIds", "title": "Entrez identifiers for genes related with an eye mutation in drosophila", "object": "drosophila", "file": "drosophila.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "recessiveIds", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "recessiveIdsEBI", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "recessiveIdsNCBI", "title": "Entrez identifiers for disease-related genes in the OMIM database", "object": "omimIds", "file": "omimIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "singh01EntrezIDs", "title": "Prostate cancer-related genes", "object": "prostateIds", "file": "prostateIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "singh05EntrezIDs", "title": "Prostate cancer-related genes", "object": "prostateIds", "file": "prostateIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "welsh01EntrezIDs", "title": "Prostate cancer-related genes", "object": "prostateIds", "file": "prostateIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "welsh05EntrezIDs", "title": "Prostate cancer-related genes", "object": "prostateIds", "file": "prostateIds.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "goProfiles-package", "title": "Performs Gene Ontology based analysis using Functional Profiles.", "topics": [ "goProfiles-package", "goProfiles" ] }, { "page": "basicProfile", "title": "Builds basic functional profile", "topics": [ "basicProfile" ] }, { "page": "CD4ids", "title": "Entrez identifiers for CD4-TCells example", "topics": [ "CD4GOTermsFrame", "CD4GOTermsList", "CD4LLids" ] }, { "page": "clustKidneyMF2", "title": "Ready 2 cluster equivalence distance matrix obtained from the analysis of the \"Kidney Dataset\" at level 2 of the MF ontology", "topics": [ "clustKidneyMF2" ] }, { "page": "compareGeneLists", "title": "Compares two lists of genes by building (expanded) profiles and comparing them", "topics": [ "compareGeneLists" ] }, { "page": "compareGOProfiles", "title": "Comparison of lists of genes through their functional profiles", "topics": [ "compareGOProfiles" ] }, { "page": "compareProfilesLists", "title": "Compares two of expanded profiles", "topics": [ "compareProfilesLists" ] }, { "page": "compSummary", "title": "This function returns a brief summary of the comparison between two (expanded) profiles.", "topics": [ "compSummary" ] }, { "page": "contractedProfile", "title": "Converts an expanded GO profile into a basic (contracted) GO profile", "topics": [ "contractedProfile", "contractedProfile.default", "contractedProfile.ExpandedGOProfile" ] }, { "page": "conversionFunctions", "title": "Functions to transformconvert objects between different types", "topics": [ "as.GOTerms.frame", "as.GOTerms.list", "BioCpack2EntrezIDS", "BioCpack2Profiles", "BioCprobes2Entrez", "GOTermsFrame2GOTermsList" ] }, { "page": "drosophila", "title": "Entrez identifiers for genes related with an eye mutation in drosophila", "topics": [ "drosophilaIds", "michaudIds", "ostrinIds" ] }, { "page": "equivalentGOProfiles", "title": "Are two lists of genes equivalent in terms of their Gene Ontology profiles?", "topics": [ "equivalentGOProfiles", "equivalentGOProfiles.default", "equivalentGOProfiles.ExpandedGOProfile", "equivalentGOProfiles.GOProfileHtest" ] }, { "page": "equivClust", "title": "For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold distance matrix and generate a dendrogram from it.", "topics": [ "equivClust" ] }, { "page": "equivClust2pdf", "title": "Save the graphical representation of objects of class 'equivClust' or 'iterEquivClust' as pdf files.", "topics": [ "equivClust2pdf", "equivClust2pdf.equivClust", "equivClust2pdf.iterEquivClust" ] }, { "page": "equivSummary", "title": "This function returns a brief summary of the equivalence test between two profiles.", "topics": [ "equivSummary" ] }, { "page": "expandedLevel", "title": "Function to create expanded levels which can contain GO Terms at different GO levels", "topics": [ "expandedLevel", "expandTerm" ] }, { "page": "expandedProfile", "title": "Builds expanded profiles", "topics": [ "expandedProfile" ] }, { "page": "fisherGOProfiles", "title": "GO Class-by-class Fisher tests in lists of genes characterized by their functional profiles", "topics": [ "fisherGOProfiles", "fisherGOProfiles.BasicGOProfile", "fisherGOProfiles.ExpandedGOProfile", "fisherGOProfiles.matrix", "fisherGOProfiles.numeric" ] }, { "page": "fitGOProfile", "title": "Does a \"sample\" GO profile 'pn', observed in a sample of 'n' genes, fit a \"population\" or \"model\" p0?", "topics": [ "fitGOProfile" ] }, { "page": "GOTermsList", "title": "Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers", "topics": [ "getAncestorsLst", "getGOLevel", "GOTermsList" ] }, { "page": "hugoIds", "title": "Entrez Identifiers obtained from the Human Genome Organization", "topics": [ "hugoIds" ] }, { "page": "iterEquivClust", "title": "For each combination of the specified levels in the choosen GO ontologies, compute the equivalence threshold distance matrix and generate a dendrogram from it.", "topics": [ "iterEquivClust" ] }, { "page": "kidneyGeneLists", "title": "Gene-lists related to kidney transplantation rejection", "topics": [ "kidneyGeneLists" ] }, { "page": "mergeProfilesLists", "title": "Combines two lists of profiles into one", "topics": [ "mergeProfilesLists" ] }, { "page": "ngenes", "title": "Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them)", "topics": [ "ngenes", "ngenes.BasicGOProfile", "ngenes.default", "ngenes.ExpandedGOProfile", "ngenes.matrix", "ngenes.numeric" ] }, { "page": "omimIds", "title": "Entrez identifiers for disease-related genes in the OMIM database", "topics": [ "diseaseIds", "dominantIds", "dominantIdsEBI", "dominantIdsNCBI", "morbidmapIds", "omimIds", "recessiveIds", "recessiveIdsEBI", "recessiveIdsNCBI" ] }, { "page": "plotProfiles", "title": "Plot functional profiles", "topics": [ "plotProfiles" ] }, { "page": "printProfiles", "title": "Print functional profiles", "topics": [ "printProfiles" ] }, { "page": "prostateIds", "title": "Prostate cancer-related genes", "topics": [ "prostateIds", "singh01EntrezIDs", "singh05EntrezIDs", "welsh01EntrezIDs", "welsh05EntrezIDs" ] } ], "_readme": "https://github.com/bioc/goProfiles/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocBaseUtils", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "CompQuadForm", "cpp11", "crayon", "curl", "DBI", "fastmap", "generics", "glue", "GO.db", "httr", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "stringi", "stringr", "sys", "vctrs", "XVector" ], "_vignettes": [ { "source": "goProfiles.Rnw", "filename": "goProfiles.pdf", "title": "goProfiles Vignette", "engine": "utils::Sweave", "headings": [ "Introduction", "Requirements", "Quick start", "User guide", "References" ], "created": "2017-10-17 15:50:36", "modified": "2018-04-17 10:58:34", "commits": 3 } ], "_score": 5.477121254719663, "_indexed": true, "_nocasepkg": "goprofiles", "_universes": [ "bioc", "alexsanchezpla" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.75.0", "date": "2026-10-09T08:18:14.000Z", "distro": "resolute", "commit": "8569caa971224ac79c322f7c854486847c011645", "fileid": 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