{ "_id": "6ab384fb3d719c1f8409090d", "Package": "annaffy", "Version": "1.85.0", "Date": "2021-06-04", "Title": "Annotation tools for Affymetrix biological metadata", "Author": "Colin A. Smith ", "Maintainer": "Colin A. Smith ", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:30:13 UTC", "RemoteUrl": "https://github.com/bioc/annaffy", "RemoteRef": "HEAD", "RemoteSha": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-23 07:38:04 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "annaffy_1.85.0.tar.gz", "_fileid": "https://r2.ropensci.org/f41127ed9e9efb133ccf8d05fb98e16c0970f5b8c07f1e5991fa4eb7942fc7fa", "_filesize": 376250, "_sha256": "f41127ed9e9efb133ccf8d05fb98e16c0970f5b8c07f1e5991fa4eb7942fc7fa", "_expires": "2027-01-01T07:51:21.000Z", "_created": "2026-09-23T07:38:04.000Z", "_published": "2026-09-23T07:51:22.907Z", "_bioccheck": { "error": 3, "warning": 6, "note": 16 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821", "_status": "success", "_upstream": "https://github.com/bioc/annaffy", "_commit": { "id": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379413 }, "_maintainer": { "name": "Colin A. Smith", "email": "colin@colinsmith.org", "login": "colinasmith", "description": "Protein Dynamics and Design", "uuid": 1170378 }, "_distro": "resolute", "_jobs": [ { "job": 107089029865, "time": 178, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "10738171480" }, { "job": 107089029956, "time": 268, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10737593397" }, { "job": 107089029920, "time": 304, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10737483590" }, { "job": 107089029881, "time": 141, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "10738356306" }, { "job": 107089029862, "time": 160, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "10737564505" }, { "job": 107087702008, "time": 280, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10737882998" }, { "job": 107089029886, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10737918346" }, { "job": 107089029917, "time": 183, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10738121707" }, { "job": 107089029928, "time": 140, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "10738146412" }, { "job": 107089029910, "time": 159, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10737818794" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.5.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "BiocManager", "role": "Depends" }, { "package": "GO.db", "role": "Depends" }, { "package": "AnnotationDbi", "version": ">= 0.1.15", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "hgu95av2.db", "role": "Suggests" }, { "package": "multtest", "role": "Suggests" }, { "package": "tcltk", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.85.0", "bioc": "3.24" }, { "branch": "release", "version": "1.84.0", "bioc": "3.23" } ], "_topics": [ "onechannel", "microarray", "annotation", "go", "pathways", "reportwriting" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 772, "source": "https://www.bioconductor.org/packages/stats/bioc/annaffy" }, "_mentions": 4, "_searchresults": 69, "_rbuild": "4.6.1", "_assets": [ "extra/annaffy.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/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" ] } ], "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocManager", "Biostrings", "bit", "bit64", "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", "vctrs", "XVector" ], "_vignettes": [ { "source": "annaffy.Rnw", "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 } ], "_score": 5.696181587168524, "_indexed": true, "_nocasepkg": "annaffy", "_universes": [ "bioc", "colinasmith" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.85.0", "date": "2026-09-23T07:41:48.000Z", "distro": "resolute", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/eb1e66174feb82fca3f84ab3395e3297822edbde121bae0af71e3aaa782e86ac", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" }, { "r": "4.6.1", "os": "linux", "version": "1.85.0", "date": "2026-09-23T07:42:19.000Z", "distro": "resolute", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/cb6a468529f77ad73e49a5f1b4dac4c5388542b7cea5ff629b09d03d499c960a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" }, { "r": "4.5.3", "os": "mac", "version": "1.85.0", "date": "2026-09-23T07:47:11.000Z", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/fb6f008f61555217878f9e94c7113c321c9aac1f55d19c6d5efeed2547059cea", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" }, { "r": "4.6.1", "os": "mac", "version": "1.85.0", "date": "2026-09-23T07:50:03.000Z", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/311cb8f58a294349ab5aa6f49f6191c5179f6649376eddf5173c10e0576f938a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" }, { "r": "4.6.0", "os": "wasm", "version": "1.85.0", "date": "2026-09-23T07:41:05.000Z", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/01c4b66f8cb820c619d90681bfad41f471b0397e76954c3d7ea451ec7ad1afc9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" }, { "r": "4.7.0", "os": "win", "version": "1.85.0", "date": "2026-09-23T07:40:15.000Z", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/cd653a9e573a2c20663900181f5671ac5addb4995ff2dfbc9671648128f2b4e6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" }, { "r": "4.5.3", "os": "win", "version": "1.85.0", "date": "2026-09-23T07:39:47.000Z", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/f978dbc7cedaa7f26d831dd8b20f0036b4cb0bbe75f3a692aa7499964febc404", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" }, { "r": "4.6.1", "os": "win", "version": "1.85.0", "date": "2026-09-23T07:39:52.000Z", "commit": "7426eeeb179fa48180b7dcac9514d9292e64a5c1", "fileid": "https://r2.ropensci.org/38404fcaed85897444415baed5b22102b9188afbb296500c75abf668fbab6654", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35832319821" } ] }