{
  "_id": "6abe429099f7aa8c6aa54738",
  "Package": "annotationTools",
  "Version": "1.86.0",
  "Date": "2020-03-27",
  "Title": "Annotate microarrays and perform cross-species gene expression\nanalyses using flat file databases",
  "Author": "Alexandre Kuhn <alexandre.m.kuhn@gmail.com>",
  "Maintainer": "Alexandre Kuhn <alexandre.m.kuhn@gmail.com>",
  "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": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:32:15 UTC",
  "RemoteUrl": "https://github.com/bioc/annotationTools",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "94865cf5b3214ace57e5a086564b07507c224119",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-01 11:15:13 UTC",
    "User": "root"
  },
  "_user": "bioc-release",
  "_type": "src",
  "_file": "annotationTools_1.86.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d52a8418dd84dbad31d780f3aff5effa339aae3fa3390da830cdf7c765d4ffd7",
  "_filesize": 498844,
  "_sha256": "d52a8418dd84dbad31d780f3aff5effa339aae3fa3390da830cdf7c765d4ffd7",
  "_expires": "2027-01-09T11:22:54.000Z",
  "_created": "2026-10-01T11:15:13.000Z",
  "_published": "2026-10-01T11:22:56.150Z",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 17
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669",
  "_status": "success",
  "_upstream": "https://github.com/bioc/annotationTools",
  "_commit": {
    "id": "94865cf5b3214ace57e5a086564b07507c224119",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to 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": 110342853016,
      "time": 129,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11157251570"
    },
    {
      "job": 110342853238,
      "time": 248,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11158031063"
    },
    {
      "job": 110342853160,
      "time": 394,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11158550388"
    },
    {
      "job": 110342853072,
      "time": 74,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11158830274"
    },
    {
      "job": 110342853129,
      "time": 86,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11158126505"
    },
    {
      "job": 110341233504,
      "time": 280,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11156722649"
    },
    {
      "job": 110342853124,
      "time": 103,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11158120672"
    },
    {
      "job": 110342853214,
      "time": 81,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11157890745"
    },
    {
      "job": 110342853435,
      "time": 72,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11158115575"
    },
    {
      "job": 110342853164,
      "time": 65,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11156459203"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_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": 471,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 622,
    "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/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt"
  ],
  "_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": false,
  "_nocasepkg": "annotationtools",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/annotationTools",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.86.0",
      "date": "2026-10-01T11:19:27.000Z",
      "distro": "resolute",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/f0a92b8994f7d1e814191cf201823215990d8fbcc3ea46e0c6896ac4afd1e7b2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.86.0",
      "date": "2026-10-01T11:21:55.000Z",
      "distro": "resolute",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/e31380da2510344a73dad313d510b3c69356f53b34a53e1102ba57b0d349b0b0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.86.0",
      "date": "2026-10-01T11:21:56.000Z",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/bfbed5ea17389599751950126feab369b952d0f619076f3e55f68a3e38e86ef6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.86.0",
      "date": "2026-10-01T11:22:13.000Z",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/747cbc56d8d5a466d7e9753deefbf27cfb9999da948d951ee89f1d91f6178814",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.86.0",
      "date": "2026-10-01T11:17:22.000Z",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/2104fd29adc6a1b85374151c6406e79afd6e8d095ef16ee3ec45fe9feb3f8431",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.86.0",
      "date": "2026-10-01T11:16:38.000Z",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/c1a1dbb66796fcc153b9018053b2cbca6165e48d92c5e7b3a7e98416ba781833",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.86.0",
      "date": "2026-10-01T11:16:30.000Z",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/5fd3260e11e2372fb1214e4a648357021d7f50bf82559c93d9df05d323ad1e16",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.86.0",
      "date": "2026-10-01T11:16:27.000Z",
      "commit": "94865cf5b3214ace57e5a086564b07507c224119",
      "fileid": "https://r2.ropensci.org/5a9f2a701efae520b87f93ca4d4deee8ca76f5ef35bad17e70f67eed00cbaa9f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/36853685669"
    }
  ]
}