{ "_id": "6a19c493acfb0bcc41dfee92", "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 ", "Maintainer": "Chris Wirth ", "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": "2026-05-29 16:47:06 UTC", "User": "root" }, "MD5sum": "e3c1964de97898df756fa6d0adc11ced", "_user": "bioc", "_type": "src", "_file": "annmap_1.55.1.tar.gz", "_fileid": "2f46a902201216b368bec25a05bdfe90f29e3d4277c723cc56fef7116a508e19", "_filesize": 959492, "_sha256": "2f46a902201216b368bec25a05bdfe90f29e3d4277c723cc56fef7116a508e19", "_created": "2026-05-29T16:47:06.000Z", "_published": "2026-05-29T16:53:39.430Z", "_jobs": [ { "job": 78546082877, "time": 201, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7296190178" }, { "job": 78546082897, "time": 296, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7296221983" }, { "job": 78546082941, "time": 314, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7296228083" }, { "job": 78546082916, "time": 201, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7296190062" }, { "job": 78546082903, "time": 171, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7296180512" }, { "job": 78545163940, "time": 337, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7296123116" }, { "job": 78546082862, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7296176858" }, { "job": 78546082913, "time": 217, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7296195285" }, { "job": 78546082891, "time": 330, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7296233522" }, { "job": 78546082904, "time": 312, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7296228448" } ], "_bioccheck": { "error": 2, "warning": 5, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/annmap", "_commit": { "id": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "Bump version to 1.55.1\n", "time": 1780071501 }, "_maintainer": { "name": "Chris Wirth", "email": "christopher.wirth@cruk.manchester.ac.uk" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.15.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "DBI", "role": "Imports" }, { "package": "RMySQL", "version": ">= 0.6-0", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "genefilter", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "rjson", "role": "Suggests" }, { "package": "Gviz", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-22", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.55.0", "bioc": "3.24" }, { "branch": "release", "version": "1.54.0", "bioc": "3.23" } ], "_topics": [ "annotation", "microarray", "onechannel", "reportwriting", "transcription", "visualization" ], "_stars": 0, "_contributors": [ { "user": "christopherwirth", "count": 5, "uuid": 11558388 }, { "user": "marek-dynowski", "count": 1, "uuid": 189386392 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 506, "source": "https://www.bioconductor.org/packages/stats/bioc/annmap" }, "_mentions": 5, "_devurl": "https://github.com/cruk-mi/annmap", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/annmap.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_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" ] }, { "page": "annmap.spliceIndex", "title": "Splice indexing", "topics": [ "spliceGroupIndex", "spliceIndex" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "digest", "fastmap", "formatR", "futile.logger", "futile.options", "genefilter", "generics", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "Rhtslib", "rlang", "RMySQL", "Rsamtools", "RSQLite", "S4Vectors", "Seqinfo", "snow", "survival", "sys", "vctrs", "XML", "xtable", "XVector" ], "_score": 3.1760912590556813, "_indexed": true, "_nocasepkg": "annmap", "_universes": [ "bioc", "cruk-mi" ], "_previous": "1.55.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.55.1", "date": "2026-05-29T16:51:00.000Z", "distro": "noble", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "b0e9aa1511acd1ad2ddc247f9307ae88f228d686b40d567261018de63573570f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" }, { "r": "4.6.0", "os": "linux", "version": "1.55.1", "date": "2026-05-29T16:51:12.000Z", "distro": "noble", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "adaa9951168a49b2807eaeb80d342a78277e7191918b464a7b9a958f7d4a6aaf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" }, { "r": "4.5.3", "os": "mac", "version": "1.55.1", "date": "2026-05-29T16:49:38.000Z", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "04980754bafce462ed6e21ad4ca3573a4ca1274c43dcbcc6bd190bb7995a4418", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" }, { "r": "4.6.0", "os": "mac", "version": "1.55.1", "date": "2026-05-29T16:49:21.000Z", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "e2d4d0bb8a2a75ce144706824ff66ab71299c871e07b35df0a637198af92f9bb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" }, { "r": "4.6.0", "os": "wasm", "version": "1.55.1", "date": "2026-05-29T16:50:29.000Z", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "1afdb10e5ae2e3348badc9d3bc3524695f3c706152745482fabd6cb29b0a20ab", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" }, { "r": "4.7.0", "os": "win", "version": "1.55.1", "date": "2026-05-29T16:49:23.000Z", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "84fa3b9cf1fafada1df2b0943e5cb05df31e66a55186c004cd7288b223bee6c7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" }, { "r": "4.5.3", "os": "win", "version": "1.55.1", "date": "2026-05-29T16:51:18.000Z", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "3f0f62915d328881cc5b0f2720957ce56ecc574ec945679779b8c2fe24963658", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" }, { "r": "4.6.0", "os": "win", "version": "1.55.1", "date": "2026-05-29T16:51:05.000Z", "commit": "6bccb78da99e75f955ccacb9ac5b4497125bc1f2", "fileid": "be8abd24bd4ef258fee990184c6da208507ba6584519ba2ed3df294bc137ca14", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26649868540" } ] }