{
  "_id": "6ae755e12e87f76f20accfc0",
  "Package": "annmap",
  "Type": "Package",
  "Title": "Genome annotation and visualisation package pertaining to\nAffymetrix arrays and NGS analysis.",
  "Description": "annmap provides annotation mappings for Affymetrix exon\narrays and coordinate based queries to support deep sequencing\ndata analysis. Database access is hidden behind the API which\nprovides a set of functions such as genesInRange(),\ngeneToExon(), exonDetails(), etc. Functions to plot gene\narchitecture and BAM file data are also provided. Underlying\ndata are from Ensembl. The annmap database can be downloaded\nfrom:\nhttps://figshare.manchester.ac.uk/account/articles/16685071",
  "Version": "1.55.1",
  "Date": "2011-09-14",
  "Author": "Tim Yates <Tim.Yates@cruk.manchester.ac.uk>",
  "Maintainer": "Chris Wirth <Christopher.Wirth@cruk.manchester.ac.uk>",
  "License": "GPL-2",
  "URL": "https://github.com/cruk-mi/annmap",
  "Collate": "zzz.R db.R utils.R cache.R statements.R filtering.R utr.R\ncoords.R ws.R plot.genomic.R plot.ngs.R si.R",
  "biocViews": "Annotation, Microarray, OneChannel, ReportWriting,\nTranscription, Visualization",
  "Config/Bioconductor/UnsupportedPlatforms": "windows",
  "Config/pak/sysreqs": "libbz2-dev liblzma-dev libmysqlclient-dev\nlibpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-29 16:18:21 UTC",
  "RemoteUrl": "https://github.com/bioc/annmap",
  "RemoteRef": "HEAD",
  "RemoteSha": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 13:21:13 UTC",
    "User": "root"
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  "_user": "bioc",
  "_type": "src",
  "_file": "annmap_1.55.1.tar.gz",
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  "_filesize": 961695,
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  "_expires": "2027-02-09T15:08:15.000Z",
  "_created": "2026-11-01T13:21:13.000Z",
  "_published": "2026-11-01T15:08:17.805Z",
  "_upstream": "https://github.com/bioc/annmap",
  "_status": "failure",
  "_maintainer": {
    "name": "Chris Wirth",
    "email": "christopher.wirth@cruk.manchester.ac.uk"
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    "author": "A Wokaty <awokaty@users.noreply.github.com>",
    "committer": "A Wokaty <awokaty@users.noreply.github.com>",
    "message": "Bump version to 1.55.1\n",
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  "_selfowned": true,
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  "_updates": [
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  "_stars": 0,
  "_contributors": [
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  "_devurl": "https://github.com/cruk-mi/annmap",
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  "_abi": {
    "exports": [
      {
        "key": "annmap::generic:domainInRange",
        "hash": "6cf3aa21df400dcb"
      },
      {
        "key": "annmap::generic:estExonInRange",
        "hash": "2f7bb04db2f2e28b"
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      {
        "key": "annmap::generic:exonInRange",
        "hash": "80b4f8abd612f688"
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      {
        "key": "annmap::generic:geneInRange",
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      {
        "key": "annmap::generic:predictionTranscriptInRange",
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      },
      {
        "key": "annmap::generic:probeInRange",
        "hash": "60b76b0565abe423"
      },
      {
        "key": "annmap::generic:probesetInRange",
        "hash": "7b88ffa746d79eaa"
      },
      {
        "key": "annmap::generic:proteinInRange",
        "hash": "39da4f1979356edb"
      },
      {
        "key": "annmap::generic:transcriptInRange",
        "hash": "89809302160c1d4d"
      }
    ],
    "imports": []
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  "_rbuild": "4.6.2",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/cruk-mi/annmap",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "allArrays",
    "allChromosomes",
    "allDomains",
    "allEstExons",
    "allEstGenes",
    "allEstTranscripts",
    "allExons",
    "allGenes",
    "allPredictionTranscripts",
    "allProbes",
    "allProbesets",
    "allProteins",
    "allSymbols",
    "allSynonyms",
    "allTranscripts",
    "annmapAddConnection",
    "annmapClearCache",
    "annmapConnect",
    "annmapDisconnect",
    "annmapEnv",
    "annmapGetParam",
    "annmapRangeApply",
    "annmapSetParam",
    "annmapToggleCaching",
    "arrayDetails",
    "arrayToProbeset",
    "arrayType",
    "chromosomeDetails",
    "codingProbesets",
    "convertBamToRle",
    "domainDetails",
    "domainInRange",
    "domainToGene",
    "domainToProbeset",
    "domainToProtein",
    "domainToTranscript",
    "estExonDetails",
    "estExonInRange",
    "estExonToEstGene",
    "estExonToEstTranscript",
    "estExonToProbeset",
    "estGeneDetails",
    "estGeneInRange",
    "estGeneToEstExon",
    "estGeneToEstTranscript",
    "estGeneToProbeset",
    "estTranscriptDetails",
    "estTranscriptInRange",
    "estTranscriptToEstExon",
    "estTranscriptToEstGene",
    "estTranscriptToProbeset",
    "exonDetails",
    "exonic",
    "exonInRange",
    "exonToGene",
    "exonToProbeset",
    "exonToTranscript",
    "geneDetails",
    "geneInRange",
    "generalisedNameToEnsembl",
    "generalisedNameToNCBI",
    "generateBridgeData",
    "geneToDomain",
    "geneToExon",
    "geneToExonProbeset",
    "geneToExonProbesetExpr",
    "geneToGeneRegionTrack",
    "geneToProbeset",
    "geneToProtein",
    "geneToSymbol",
    "geneToSynonym",
    "geneToTranscript",
    "genomeToProteinCoords",
    "genomeToTranscriptCoords",
    "genomicExonDepthPlot",
    "genomicPlot",
    "genomicProbePlot",
    "hasProbes",
    "hasProbesAtleast",
    "hasProbesBetween",
    "hasProbesIn",
    "intergenic",
    "intronic",
    "isExonic",
    "isIntergenic",
    "isIntronic",
    "isUnreliable",
    "ngsBridgePlot",
    "ngsTraceLabel",
    "ngsTracePlotter",
    "ngsTraceScale",
    "nonIntronicGeneLength",
    "nonIntronicTranscriptLength",
    "predictionTranscriptDetails",
    "predictionTranscriptInRange",
    "predictionTranscriptToPredictionExon",
    "predictionTranscriptToProbeset",
    "probeDetails",
    "probeInRange",
    "probesetDetails",
    "probesetInRange",
    "probesetToCdnatranscript",
    "probesetToDomain",
    "probesetToEstExon",
    "probesetToEstGene",
    "probesetToEstTranscript",
    "probesetToExon",
    "probesetToGene",
    "probesetToHit",
    "probesetToPredictionTranscript",
    "probesetToProbe",
    "probesetToProtein",
    "probesetToTranscript",
    "probeToHit",
    "probeToProbeset",
    "proteinCoordsToGenome",
    "proteinDetails",
    "proteinInRange",
    "proteinToDomain",
    "proteinToGene",
    "proteinToProbeset",
    "proteinToTranscript",
    "seqnameMapping",
    "seqnamesToEnsembl",
    "seqnamesToNCBI",
    "spliceGroupIndex",
    "spliceIndex",
    "strandAsInteger",
    "symbolToEstGene",
    "symbolToEstTranscript",
    "symbolToGene",
    "symbolToTranscript",
    "synonymDetails",
    "synonymToEstGene",
    "synonymToEstTranscript",
    "synonymToGene",
    "synonymToTranscript",
    "transcriptCoordsToGenome",
    "transcriptDetails",
    "transcriptInRange",
    "transcriptToCdnaprobeset",
    "transcriptToCodingExon",
    "transcriptToCodingRange",
    "transcriptToDomain",
    "transcriptToExon",
    "transcriptToExonProbeset",
    "transcriptToGene",
    "transcriptToProbeset",
    "transcriptToProtein",
    "transcriptToSynonym",
    "transcriptToTranslatedprobes",
    "transcriptToUtrExon",
    "transcriptToUtrRange",
    "unreliable",
    "utrProbesets"
  ],
  "_help": [
    {
      "page": "annmap-package",
      "title": "Provide access to the Annmap annotation database",
      "topics": [
        "annmap-package",
        "annmap"
      ]
    },
    {
      "page": "annmap.all",
      "title": "annmap 'all' functions",
      "topics": [
        "allArrays",
        "allChromosomes",
        "allDomains",
        "allEstExons",
        "allEstGenes",
        "allEstTranscripts",
        "allExons",
        "allGenes",
        "allPredictionTranscripts",
        "allProbes",
        "allProbesets",
        "allProteins",
        "allSymbols",
        "allSynonyms",
        "allTranscripts",
        "annmapAll"
      ]
    },
    {
      "page": "annmap.coords",
      "title": "annmap co-ordinate mapping functions",
      "topics": [
        "genomeToProteinCoords",
        "genomeToTranscriptCoords",
        "proteinCoordsToGenome",
        "transcriptCoordsToGenome"
      ]
    },
    {
      "page": "annmap.details",
      "title": "annmap 'details' functions",
      "topics": [
        "annmapDetails",
        "arrayDetails",
        "chromosomeDetails",
        "domainDetails",
        "estExonDetails",
        "estGeneDetails",
        "estTranscriptDetails",
        "exonDetails",
        "geneDetails",
        "predictionTranscriptDetails",
        "probeDetails",
        "probesetDetails",
        "proteinDetails",
        "synonymDetails",
        "transcriptDetails"
      ]
    },
    {
      "page": "annmap.env",
      "title": "annmap 'env' functions",
      "topics": [
        "annmapEnv",
        "annmapGetParam",
        "annmapSetParam"
      ]
    },
    {
      "page": "annmap.filters",
      "title": "annmap 'filter' functions",
      "topics": [
        "annmapFilters",
        "exonic",
        "hasProbes",
        "hasProbesAtleast",
        "hasProbesBetween",
        "hasProbesIn",
        "intergenic",
        "intronic",
        "isExonic",
        "isIntergenic",
        "isIntronic",
        "isUnreliable",
        "unreliable"
      ]
    },
    {
      "page": "annmap.range",
      "title": "annmap 'range' functions",
      "topics": [
        "annmapRange",
        "domainInRange",
        "domainInRange,character-method",
        "domainInRange,data.frame-method",
        "domainInRange,factor-method",
        "domainInRange,GRanges-method",
        "domainInRange,NULL-method",
        "domainInRange,RangedData-method",
        "estExonInRange",
        "estExonInRange,character-method",
        "estExonInRange,data.frame-method",
        "estExonInRange,factor-method",
        "estExonInRange,GRanges-method",
        "estExonInRange,NULL-method",
        "estExonInRange,RangedData-method",
        "estGeneInRange",
        "estGeneInRange,character-method",
        "estGeneInRange,data.frame-method",
        "estGeneInRange,factor-method",
        "estGeneInRange,GRanges-method",
        "estGeneInRange,NULL-method",
        "estGeneInRange,RangedData-method",
        "estTranscriptInRange",
        "estTranscriptInRange,character-method",
        "estTranscriptInRange,data.frame-method",
        "estTranscriptInRange,factor-method",
        "estTranscriptInRange,GRanges-method",
        "estTranscriptInRange,NULL-method",
        "estTranscriptInRange,RangedData-method",
        "exonInRange",
        "exonInRange,character-method",
        "exonInRange,data.frame-method",
        "exonInRange,factor-method",
        "exonInRange,GRanges-method",
        "exonInRange,NULL-method",
        "exonInRange,RangedData-method",
        "geneInRange",
        "geneInRange,character-method",
        "geneInRange,data.frame-method",
        "geneInRange,factor-method",
        "geneInRange,GRanges-method",
        "geneInRange,NULL-method",
        "geneInRange,RangedData-method",
        "predictionTranscriptInRange",
        "predictionTranscriptInRange,character-method",
        "predictionTranscriptInRange,data.frame-method",
        "predictionTranscriptInRange,factor-method",
        "predictionTranscriptInRange,GRanges-method",
        "predictionTranscriptInRange,NULL-method",
        "predictionTranscriptInRange,RangedData-method",
        "probeInRange",
        "probeInRange,character-method",
        "probeInRange,data.frame-method",
        "probeInRange,factor-method",
        "probeInRange,GRanges-method",
        "probeInRange,NULL-method",
        "probeInRange,RangedData-method",
        "probesetInRange",
        "probesetInRange,character-method",
        "probesetInRange,data.frame-method",
        "probesetInRange,factor-method",
        "probesetInRange,GRanges-method",
        "probesetInRange,NULL-method",
        "probesetInRange,RangedData-method",
        "proteinInRange",
        "proteinInRange,character-method",
        "proteinInRange,data.frame-method",
        "proteinInRange,factor-method",
        "proteinInRange,GRanges-method",
        "proteinInRange,NULL-method",
        "proteinInRange,RangedData-method",
        "transcriptInRange",
        "transcriptInRange,character-method",
        "transcriptInRange,data.frame-method",
        "transcriptInRange,factor-method",
        "transcriptInRange,GRanges-method",
        "transcriptInRange,NULL-method",
        "transcriptInRange,RangedData-method"
      ]
    },
    {
      "page": "annmap.seqname",
      "title": "Seqnames manipulation functions",
      "topics": [
        "annmapSeqname",
        "generalisedNameToEnsembl",
        "generalisedNameToNCBI",
        "seqnameMapping",
        "seqnamesToEnsembl",
        "seqnamesToNCBI"
      ]
    },
    {
      "page": "annmap.to",
      "title": "annmap 'to' functions",
      "topics": [
        "annmapTo",
        "arrayToProbeset",
        "domainToGene",
        "domainToProbeset",
        "domainToProtein",
        "domainToTranscript",
        "estExonToEstGene",
        "estExonToEstTranscript",
        "estExonToProbeset",
        "estGeneToEstExon",
        "estGeneToEstTranscript",
        "estGeneToProbeset",
        "estTranscriptToEstExon",
        "estTranscriptToEstGene",
        "estTranscriptToProbeset",
        "exonToGene",
        "exonToProbeset",
        "exonToTranscript",
        "geneToDomain",
        "geneToExon",
        "geneToExonProbeset",
        "geneToExonProbesetExpr",
        "geneToProbeset",
        "geneToProtein",
        "geneToSymbol",
        "geneToSynonym",
        "geneToTranscript",
        "predictionTranscriptToPredictionExon",
        "predictionTranscriptToProbeset",
        "probesetToCdnatranscript",
        "probesetToDomain",
        "probesetToEstExon",
        "probesetToEstGene",
        "probesetToEstTranscript",
        "probesetToExon",
        "probesetToGene",
        "probesetToHit",
        "probesetToPredictionTranscript",
        "probesetToProbe",
        "probesetToProtein",
        "probesetToTranscript",
        "probeToHit",
        "probeToProbeset",
        "proteinToDomain",
        "proteinToGene",
        "proteinToProbeset",
        "proteinToTranscript",
        "symbolToEstGene",
        "symbolToEstTranscript",
        "symbolToGene",
        "symbolToTranscript",
        "synonymToEstGene",
        "synonymToEstTranscript",
        "synonymToGene",
        "synonymToTranscript",
        "transcriptToCdnaprobeset",
        "transcriptToDomain",
        "transcriptToExon",
        "transcriptToExonProbeset",
        "transcriptToGene",
        "transcriptToProbeset",
        "transcriptToProtein",
        "transcriptToSynonym",
        "transcriptToTranslatedprobes"
      ]
    },
    {
      "page": "annmap.utils",
      "title": "annmap 'utils' functions",
      "topics": [
        "annmapAddConnection",
        "annmapClearCache",
        "annmapConnect",
        "annmapDisconnect",
        "annmapGenePlot",
        "annmapRangeApply",
        "annmapToggleCaching",
        "annmapUtils",
        "arrayType",
        "geneToGeneRegionTrack",
        "strandAsInteger"
      ]
    },
    {
      "page": "annmap.utr",
      "title": "annmap coding functions",
      "topics": [
        "codingProbesets",
        "nonIntronicGeneLength",
        "nonIntronicTranscriptLength",
        "transcriptToCodingExon",
        "transcriptToCodingRange",
        "transcriptToUtrExon",
        "transcriptToUtrRange",
        "utrProbesets"
      ]
    },
    {
      "page": "plot.genomic",
      "title": "Plotting a section of a chromosome.",
      "topics": [
        "genomicExonDepthPlot",
        "genomicPlot",
        "genomicProbePlot"
      ]
    },
    {
      "page": "plot.ngs",
      "title": "Plotting BAM file data alongside the features of a chromosome",
      "topics": [
        "convertBamToRle",
        "generateBridgeData",
        "ngsBridgePlot",
        "ngsTraceLabel",
        "ngsTracePlotter",
        "ngsTraceScale"
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