{ "_id": "6a5323969b92047c28d55b15", "Package": "annotationTools", "Version": "1.87.0", "Date": "2020-03-27", "Title": "Annotate microarrays and perform cross-species gene expression\nanalyses using flat file databases", "Author": "Alexandre Kuhn ", "Maintainer": "Alexandre Kuhn ", "Description": "Functions to annotate microarrays, find orthologs, and\nintegrate heterogeneous gene expression profiles using\nannotation and other molecular biology information available as\nflat file database (plain text files).", "biocViews": "Microarray, Annotation", "License": "GPL", "ZipData": "no", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:32:15 UTC", "RemoteUrl": "https://github.com/bioc/annotationTools", "RemoteRef": "HEAD", "RemoteSha": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-12 05:14:10 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "annotationTools_1.87.0.tar.gz", "_fileid": "https://r2.ropensci.org/e56deb77c286414218cc3ce86957c78f9e8771cd8a32fb63dac426bcc134af9d", "_filesize": 497679, "_sha256": "e56deb77c286414218cc3ce86957c78f9e8771cd8a32fb63dac426bcc134af9d", "_expires": "2026-10-20T05:18:12.000Z", "_created": "2026-07-12T05:14:10.000Z", "_published": "2026-07-12T05:18:13.969Z", "_bioccheck": { "error": 1, "warning": 4, "note": 17 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001", "_status": "success", "_upstream": "https://github.com/bioc/annotationTools", "_commit": { "id": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379535 }, "_maintainer": { "name": "Alexandre Kuhn", "email": "alexandre.m.kuhn@gmail.com", "login": "alexandremkuhn", "description": "", "uuid": 12440122 }, "_distro": "resolute", "_jobs": [ { "job": 86618102145, "time": 146, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8256357768" }, { "job": 86618102149, "time": 205, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8256365790" }, { "job": 86618102148, "time": 197, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8256364576" }, { "job": 86618102146, "time": 90, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8256350133" }, { "job": 86618102139, "time": 104, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8256351899" }, { "job": 86617801398, "time": 262, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8256337518" }, { "job": 86618102131, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8256355336" }, { "job": 86618102140, "time": 79, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8256348761" }, { "job": 86618102158, "time": 81, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8256349142" }, { "job": 86618102153, "time": 82, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8256349151" } ], "_registered": true, "_dependencies": [ { "package": "Biobase", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.87.0", "bioc": "3.24" }, { "branch": "release", "version": "1.86.0", "bioc": "3.23" } ], "_topics": [ "microarray", "annotation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 562, "source": "https://www.bioconductor.org/packages/stats/bioc/annotationTools" }, "_mentions": 3, "_searchresults": 24, "_rbuild": "4.6.1", "_assets": [ "extra/annotationTools.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "compactList", "getANNOTATION", "getGENEID", "getGENEONTOLOGY", "getGENESYMBOL", "getGENETITLE", "getHOMOLOG", "getMULTIANNOTATION", "getOrthologousProbesets", "getPROBESET", "listToCharacterVector", "ps2ps" ], "_datasets": [ { "name": "annot_HGU133A", "title": "annot\\_HGU133A", "object": "orthologs_example", "file": "orthologs_example.RData", "class": [ "data.frame" ], "fields": [ "Probe.Set.ID", "GeneChip.Array", "Species.Scientific.Name", "Annotation.Date", "Sequence.Type", "Sequence.Source", "Transcript.ID.Array.Design.", "Target.Description", "Representative.Public.ID", "Archival.UniGene.Cluster", "UniGene.ID", "Genome.Version", "Alignments", "Gene.Title", "Gene.Symbol", "Chromosomal.Location", "Unigene.Cluster.Type", "Ensembl", "Entrez.Gene", "SwissProt", "EC", "OMIM", "RefSeq.Protein.ID", "RefSeq.Transcript.ID", "FlyBase", "AGI", "WormBase", "MGI.Name", "RGD.Name", "SGD.accession.number", "Gene.Ontology.Biological.Process", "Gene.Ontology.Cellular.Component", "Gene.Ontology.Molecular.Function", "Pathway", "Protein.Families", "Protein.Domains", "InterPro", "Trans.Membrane", "QTL", "Annotation.Description", "Annotation.Transcript.Cluster", "Transcript.Assignments", "Annotation.Notes" ], "rows": 188, "table": true, "tojson": true }, { "name": "ortho", "title": "ortho", "object": "orthologs_example", "file": "orthologs_example.RData", "class": [ "data.frame" ], "fields": [ "ps1", "gid1", "gid2", "ps2" ], "rows": 100, "table": true, "tojson": true }, { "name": "table_human", "title": "table\\_human", "object": "orthologs_example", "file": "orthologs_example.RData", "class": [ "data.frame" ], "fields": [ "Caudate", "log2FC.HD.caudate.grade.0.2.vs.controls", "t.caudate", "P.Value.caudate", "Chip", "Probe.Set.ID", "UniGene.ID", "Gene.Title", "Gene.Symbol", "Gene.Ontology.Biological.Process", "Gene.Ontology.Cellular.Component", "Gene.Ontology.Molecular.Function" ], "rows": 188, "table": true, "tojson": true }, { "name": "table_mouse", "title": "table\\_mouse", "object": "orthologs_example", "file": "orthologs_example.RData", "class": [ "data.frame" ], "fields": [ "Name", "M", "t", "P.Value", "X", "Probe.Set.ID", "Title", "Gene.Symbol" ], "rows": 100, "table": true, "tojson": true } ], "_help": [ { "page": "annot_HGU133A", "title": "annot\\_HGU133A", "topics": [ "annot_HGU133A" ] }, { "page": "compactList", "title": "Concatenate list elements", "topics": [ "compactList" ] }, { "page": "gene_orthologs_part", "title": "Example gene_orthologs file", "topics": [ "gene_orthologs_part" ] }, { "page": "getANNOTATION", "title": "General annotation function", "topics": [ "getANNOTATION" ] }, { "page": "getGENEID", "title": "Find gene IDs", "topics": [ "getGENEID" ] }, { "page": "getGENEONTOLOGY", "title": "Find Gene Ontology (GO) annotation", "topics": [ "getGENEONTOLOGY" ] }, { "page": "getGENESYMBOL", "title": "Find gene symbols", "topics": [ "getGENESYMBOL" ] }, { "page": "getGENETITLE", "title": "Find gene titles", "topics": [ "getGENETITLE" ] }, { "page": "getHOMOLOG", "title": "Find homologous/orthologous gene (ID)", "topics": [ "getHOMOLOG" ] }, { "page": "getMULTIANNOTATION", "title": "General (multiple) annotation function", "topics": [ "getMULTIANNOTATION" ] }, { "page": "getOrthologousProbesets", "title": "Find orthologous/homologous probe sets present in a target set using a mapping table", "topics": [ "getOrthologousProbesets" ] }, { "page": "getPROBESET", "title": "Find probe set IDs", "topics": [ "getPROBESET" ] }, { "page": "HG-U133_Plus_2_annot_part", "title": "Example Affymetrix annotation file", "topics": [ "HG-U133_Plus_2_annot_part" ] }, { "page": "HG-U133_Plus_2_ortholog_part", "title": "Example Affymetrix ortholog file", "topics": [ "HG-U133_Plus_2_ortholog_part" ] }, { "page": "homologene_part", "title": "Example HomoloGene file", "topics": [ "homologene_part" ] }, { "page": "listToCharacterVector", "title": "Turn list into character vector", "topics": [ "listToCharacterVector" ] }, { "page": "Mouse430_2_annot_part", "title": "Example Affymetrix annotation file", "topics": [ "Mouse430_2_annot_part" ] }, { "page": "ortho", "title": "ortho", "topics": [ "ortho" ] }, { "page": "ps2ps", "title": "Find orthologous/homologous probe sets across two different Affymetrix microarray formats using a table of orthologs", "topics": [ "ps2ps" ] }, { "page": "table_human", "title": "table\\_human", "topics": [ "table_human" ] }, { "page": "table_mouse", "title": "table\\_mouse", "topics": [ "table_mouse" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics" ], "_vignettes": [ { "source": "annotationTools.Rnw", "filename": "annotationTools.pdf", "title": "annotationTools: Overview", "engine": "utils::Sweave", "headings": [ "1 Introduction", "2 Annotation", "3 Find orthologs", "4 Build tables of orthologous probe sets", "5 An example cross-species analysis of gene expression: Transcriptional dysregulation in Huntington's disease patients and in a genetic mouse model", "6 Session Information" ], "created": "2013-11-01 19:59:38", "modified": "2020-03-29 09:30:21", "commits": 7 } ], "_score": 4.635483746814913, "_indexed": true, "_nocasepkg": "annotationtools", "_universes": [ "bioc", "alexandremkuhn" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.87.0", "date": "2026-07-12T05:17:40.000Z", "distro": "resolute", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/88a293d3573799405f5bf5ca5b32dd1e03caf061d2b99c37de6a0ed9f5e4d121", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" }, { "r": "4.6.1", "os": "linux", "version": "1.87.0", "date": "2026-07-12T05:17:27.000Z", "distro": "resolute", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/1eb33496081e40a4fdb76f7441981360092dd592089e3d73c7ec934d072bbef3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" }, { "r": "4.5.3", "os": "mac", "version": "1.87.0", "date": "2026-07-12T05:15:46.000Z", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/9405ed0b5f26c344a6c6145ae327444e477a166d8f32e214db95edbc8188a028", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" }, { "r": "4.6.1", "os": "mac", "version": "1.87.0", "date": "2026-07-12T05:15:55.000Z", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/dbba46acd87fcbb46f5048bcba0d096a1ee8725804788f2e0440efb523142b8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" }, { "r": "4.6.0", "os": "wasm", "version": "1.87.0", "date": "2026-07-12T05:16:37.000Z", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/75381dc5927441816fbc8a3e9ddb97fe3fdddf8ab7a237f7334e46002bdb3d54", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" }, { "r": "4.7.0", "os": "win", "version": "1.87.0", "date": "2026-07-12T05:15:27.000Z", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/b79c8c6a4739abc70492c2acd99fea3634b0a4ff87ab3e27efd834355dbfd30d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" }, { "r": "4.5.3", "os": "win", "version": "1.87.0", "date": "2026-07-12T05:15:32.000Z", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/d57865a46389df692bb18ddcdaac7f75038a6dc7b8cae1952f78f7b358bcee07", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" }, { "r": "4.6.1", "os": "win", "version": "1.87.0", "date": "2026-07-12T05:15:28.000Z", "commit": "f13657d7c8d0092faaea187d8ba17006b5a898d2", "fileid": "https://r2.ropensci.org/b14212c2def2f12434d09568ff7278321b9bec6071b84dac7d85297dd9bff1bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29180764001" } ] }