{
  "_id": "6a3635803efcd9bda43f77f1",
  "Package": "annaffy",
  "Version": "1.84.0",
  "Date": "2021-06-04",
  "Title": "Annotation tools for Affymetrix biological metadata",
  "Author": "Colin A. Smith <colin@colinsmith.org>",
  "Maintainer": "Colin A. Smith <colin@colinsmith.org>",
  "Description": "Functions for handling data from Bioconductor Affymetrix\nannotation data packages. Produces compact HTML and text\nreports including experimental data and URL links to many\nonline databases. Allows searching biological metadata using\nvarious criteria.",
  "License": "LGPL",
  "LazyLoad": "yes",
  "biocViews": "OneChannel, Microarray, Annotation, GO, Pathways,\nReportWriting",
  "Config/pak/sysreqs": "libpng-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:30:13 UTC",
  "RemoteUrl": "https://github.com/bioc/annaffy",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "88951c07135d27b88fdb9a8fca21fab8d1d5fb7d",
  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "_user": "bioc-release",
  "_type": "src",
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  "_published": "2026-06-20T06:38:56.188Z",
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    "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",
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    "name": "Colin A. Smith",
    "email": "colin@colinsmith.org",
    "login": "colinasmith",
    "description": "Protein Dynamics and Design",
    "uuid": 1170378
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    },
    {
      "package": "BiocManager",
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      "role": "Suggests"
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      "role": "Suggests"
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      "role": "Suggests"
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      "bioc": "3.24"
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    {
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      "version": "1.84.0",
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    }
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    "microarray",
    "annotation",
    "go",
    "pathways",
    "reportwriting"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "extra/citation.cff",
    "extra/citation.html",
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    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aaf.handler",
    "aafChromLoc",
    "aafChromosome",
    "aafCytoband",
    "aafDescription",
    "aafGenBank",
    "aafGO",
    "aafLocusLink",
    "aafPathway",
    "aafProbe",
    "aafPubMed",
    "aafSearchGO",
    "aafSearchText",
    "aafSymbol",
    "aafTable",
    "aafTableAnn",
    "aafTableFrame",
    "aafTableInt",
    "colnames",
    "getCSS",
    "getHTML",
    "getTD",
    "getText",
    "getURL",
    "is.annpkg",
    "probeids",
    "probeids<-",
    "saveHTML",
    "saveText",
    "selectorWidget",
    "show"
  ],
  "_datasets": [
    {
      "name": "aafExpr",
      "title": "Sample ExpressionSet used for demonstration purposes",
      "object": "aafExpr",
      "file": "aafExpr.rda",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "aaf.handler",
      "title": "Handle feching annotation data columns",
      "topics": [
        "aaf.handler"
      ]
    },
    {
      "page": "aafChromLoc",
      "title": "Constructor for aafChromLoc objects",
      "topics": [
        "aafChromLoc"
      ]
    },
    {
      "page": "aafChromLoc-class",
      "title": "Class aafChromLoc, a class for gene chromosome locations",
      "topics": [
        "aafChromLoc-class"
      ]
    },
    {
      "page": "aafChromosome",
      "title": "Constructor for aafChromosome objects",
      "topics": [
        "aafChromosome"
      ]
    },
    {
      "page": "aafChromosome-class",
      "title": "Class aafChromosome, a class for gene chromosome assignments",
      "topics": [
        "aafChromosome-class"
      ]
    },
    {
      "page": "aafCytoband",
      "title": "Constructor for aafCytoband objects",
      "topics": [
        "aafCytoband"
      ]
    },
    {
      "page": "aafCytoband-class",
      "title": "Class aafCytoband, a class for cytoband data",
      "topics": [
        "aafCytoband-class",
        "getText,aafCytoband-method",
        "getURL,aafCytoband-method",
        "show,aafCytoband-method"
      ]
    },
    {
      "page": "aafDescription",
      "title": "Constructor for aafDescription objects",
      "topics": [
        "aafDescription"
      ]
    },
    {
      "page": "aafDescription-class",
      "title": "Class aafDescription, a class for gene descriptions",
      "topics": [
        "aafDescription-class"
      ]
    },
    {
      "page": "aafExpr",
      "title": "Sample ExpressionSet used for demonstration purposes",
      "topics": [
        "aafExpr"
      ]
    },
    {
      "page": "aafGenBank",
      "title": "Constructor for aafGenBank objects",
      "topics": [
        "aafGenBank"
      ]
    },
    {
      "page": "aafGenBank-class",
      "title": "Class aafGenBank, a class for GenBank accession numbers",
      "topics": [
        "aafGenBank-class",
        "getURL,aafGenBank-method"
      ]
    },
    {
      "page": "aafGO",
      "title": "Constructor for aafGO objects",
      "topics": [
        "aafGO"
      ]
    },
    {
      "page": "aafGO-class",
      "title": "Class aafGO, a class for gene ontology ids",
      "topics": [
        "aafGO-class",
        "getCSS,aafGO-method",
        "getHTML,aafGO-method",
        "getTD,aafGO-method",
        "getText,aafGO-method",
        "getURL,aafGO-method"
      ]
    },
    {
      "page": "aafGOItem-class",
      "title": "Class aafGOItem, a class for gene ontology id elements",
      "topics": [
        "aafGOItem",
        "aafGOItem-class",
        "getHTML,aafGOItem-method",
        "getText,aafGOItem-method",
        "getURL,aafGOItem-method",
        "show,aafGOItem-method"
      ]
    },
    {
      "page": "aafIntensity-class",
      "title": "Class aafIntensity, a class for gene expression values",
      "topics": [
        "aafIntensity",
        "aafIntensity-class",
        "getTD,aafIntensity-method"
      ]
    },
    {
      "page": "aafList-class",
      "title": "Class aafList, a specialized subclass of list",
      "topics": [
        "aafList",
        "aafList-class",
        "getCSS,aafList-method",
        "getHTML,aafList-method",
        "getTD,aafList-method",
        "getText,aafList-method",
        "getURL,aafList-method",
        "show,aafList-method",
        "[,aafList-method"
      ]
    },
    {
      "page": "aafLocusLink",
      "title": "Constructor for aafLocusLink objects",
      "topics": [
        "aafLocusLink"
      ]
    },
    {
      "page": "aafLocusLink-class",
      "title": "Class aafLocusLink, a class for LocusLink ids",
      "topics": [
        "aafLocusLink-class",
        "getURL,aafLocusLink-method"
      ]
    },
    {
      "page": "aafPathway",
      "title": "Constructor for aafPathway objects",
      "topics": [
        "aafPathway"
      ]
    },
    {
      "page": "aafPathway-class",
      "title": "Class aafPathway, a class for KEGG pathway ids",
      "topics": [
        "aafPathway-class",
        "getCSS,aafPathway-method",
        "getHTML,aafPathway-method",
        "getTD,aafPathway-method",
        "getText,aafPathway-method",
        "getURL,aafPathway-method"
      ]
    },
    {
      "page": "aafPathwayItem-class",
      "title": "Class aafPathwayItem, a class for KEGG pathway id elements",
      "topics": [
        "aafPathwayItem",
        "aafPathwayItem-class",
        "getHTML,aafPathwayItem-method",
        "getText,aafPathwayItem-method",
        "getURL,aafPathwayItem-method",
        "show,aafPathwayItem-method"
      ]
    },
    {
      "page": "aafProbe",
      "title": "Constructor for aafProbe objects",
      "topics": [
        "aafProbe"
      ]
    },
    {
      "page": "aafProbe-class",
      "title": "Class aafProbe, a class for Probe ids",
      "topics": [
        "aafProbe-class",
        "getURL,aafProbe-method"
      ]
    },
    {
      "page": "aafPubMed",
      "title": "Constructor for aafPubMed objects",
      "topics": [
        "aafPubMed"
      ]
    },
    {
      "page": "aafPubMed-class",
      "title": "Class aafPubMed, a class for PubMed ids",
      "topics": [
        "aafPubMed-class",
        "getCSS,aafPubMed-method",
        "getHTML,aafPubMed-method",
        "getTD,aafPubMed-method",
        "getURL,aafPubMed-method"
      ]
    },
    {
      "page": "aafSearchGO",
      "title": "Find probe ids corresponding to GO ids",
      "topics": [
        "aafSearchGO"
      ]
    },
    {
      "page": "aafSearchText",
      "title": "Search metadata annotation text",
      "topics": [
        "aafSearchText"
      ]
    },
    {
      "page": "aafSigned-class",
      "title": "Class aafSigned, a class for signed numerical data",
      "topics": [
        "aafSigned",
        "aafSigned-class",
        "getCSS,aafSigned-method",
        "getTD,aafSigned-method"
      ]
    },
    {
      "page": "aafSymbol",
      "title": "Constructor for aafSymbol objects",
      "topics": [
        "aafSymbol"
      ]
    },
    {
      "page": "aafSymbol-class",
      "title": "Class aafSymbol, a class for gene symbols",
      "topics": [
        "aafSymbol-class"
      ]
    },
    {
      "page": "aafTable",
      "title": "Constructor for aafTable objects",
      "topics": [
        "aafTable"
      ]
    },
    {
      "page": "aafTable-class",
      "title": "Class aafTable, a tabular microarray data class",
      "topics": [
        "$.aafTable",
        "aafTable-class",
        "colnames",
        "colnames,aafTable-method",
        "colnames<-",
        "colnames<-,aafTable-method",
        "dim.aafTable",
        "merge.aafTable",
        "probeids",
        "probeids,aafTable-method",
        "probeids<-",
        "probeids<-,aafTable-method",
        "rbind.aafTable",
        "saveHTML",
        "saveHTML,aafTable-method",
        "saveText",
        "saveText,aafTable-method",
        "[,aafTable-method",
        "[[,aafTable-method"
      ]
    },
    {
      "page": "aafTableAnn",
      "title": "Constructor for aafTable objects from annotation data",
      "topics": [
        "aafTableAnn"
      ]
    },
    {
      "page": "aafTableFrame",
      "title": "Constructor for aafTable objects from data frames",
      "topics": [
        "aafTableFrame"
      ]
    },
    {
      "page": "aafTableInt",
      "title": "Constructor for aafTable objects from ExpressionSets",
      "topics": [
        "aafTableInt"
      ]
    },
    {
      "page": "getCSS-methods",
      "title": "Methods for function getCSS",
      "topics": [
        "getCSS",
        "getCSS,ANY-method",
        "getCSS-methods"
      ]
    },
    {
      "page": "getHTML-methods",
      "title": "Methods for function getHTML",
      "topics": [
        "getHTML",
        "getHTML,ANY-method",
        "getHTML-methods"
      ]
    },
    {
      "page": "getTD-methods",
      "title": "Methods for function getTD",
      "topics": [
        "getTD",
        "getTD,ANY-method",
        "getTD-methods"
      ]
    },
    {
      "page": "getText-methods",
      "title": "Methods for function getText",
      "topics": [
        "getText",
        "getText,ANY-method",
        "getText-methods"
      ]
    },
    {
      "page": "getURL-methods",
      "title": "Methods for function getURL",
      "topics": [
        "getURL",
        "getURL,ANY-method",
        "getURL-methods"
      ]
    },
    {
      "page": "is.annpkg",
      "title": "Determine if packages contain annotation",
      "topics": [
        "is.annpkg"
      ]
    },
    {
      "page": "selectorWidget",
      "title": "Dialog to select items from a list",
      "topics": [
        "selectorWidget"
      ]
    }
  ],
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    "Biobase",
    "BiocGenerics",
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    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "generics",
    "glue",
    "GO.db",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lifecycle",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "sys",
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    "XVector"
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      "filename": "annaffy.pdf",
      "title": "annaffy Primer",
      "engine": "utils::Sweave",
      "headings": [
        "Loading Annotation Data",
        "Linking to Online Databases",
        "Building HTML Pages",
        "Searching Metadata"
      ],
      "created": "2013-11-01 19:49:39",
      "modified": "2021-01-26 22:09:25",
      "commits": 3
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  ],
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  "_nocasepkg": "annaffy",
  "_universes": [
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  "_indexurl": "https://bioc.r-universe.dev/annaffy",
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