Package: annmap 1.49.0
Chris Wirth
annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071
Authors:
annmap_1.49.0.tar.gz
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annmap.pdf |annmap.html✨
annmap/json (API)
NEWS
| # Install 'annmap' in R: |
| install.packages('annmap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cruk-mi/annmap/issues
On BioConductor:annmap-1.47.0(bioc 3.20)annmap-1.46.0(bioc 3.19)
annotationmicroarrayonechannelreportwritingtranscriptionvisualization
Last updated 23 days agofrom:da770e6b0e. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 30 2024 |
| R-4.5-win | WARNING | Oct 30 2024 |
| R-4.5-linux | WARNING | Oct 30 2024 |
| R-4.4-win | WARNING | Oct 30 2024 |
| R-4.4-mac | WARNING | Oct 30 2024 |
| R-4.3-win | WARNING | Oct 30 2024 |
| R-4.3-mac | WARNING | Oct 30 2024 |
Exports:allArraysallChromosomesallDomainsallEstExonsallEstGenesallEstTranscriptsallExonsallGenesallPredictionTranscriptsallProbesallProbesetsallProteinsallSymbolsallSynonymsallTranscriptsannmapAddConnectionannmapClearCacheannmapConnectannmapDisconnectannmapEnvannmapGetParamannmapRangeApplyannmapSetParamannmapToggleCachingarrayDetailsarrayToProbesetarrayTypechromosomeDetailscodingProbesetsconvertBamToRledomainDetailsdomainInRangedomainToGenedomainToProbesetdomainToProteindomainToTranscriptestExonDetailsestExonInRangeestExonToEstGeneestExonToEstTranscriptestExonToProbesetestGeneDetailsestGeneInRangeestGeneToEstExonestGeneToEstTranscriptestGeneToProbesetestTranscriptDetailsestTranscriptInRangeestTranscriptToEstExonestTranscriptToEstGeneestTranscriptToProbesetexonDetailsexonicexonInRangeexonToGeneexonToProbesetexonToTranscriptgeneDetailsgeneInRangegeneralisedNameToEnsemblgeneralisedNameToNCBIgenerateBridgeDatageneToDomaingeneToExongeneToExonProbesetgeneToExonProbesetExprgeneToGeneRegionTrackgeneToProbesetgeneToProteingeneToSymbolgeneToSynonymgeneToTranscriptgenomeToProteinCoordsgenomeToTranscriptCoordsgenomicExonDepthPlotgenomicPlotgenomicProbePlothasProbeshasProbesAtleasthasProbesBetweenhasProbesInintergenicintronicisExonicisIntergenicisIntronicisUnreliablengsBridgePlotngsTraceLabelngsTracePlotterngsTraceScalenonIntronicGeneLengthnonIntronicTranscriptLengthpredictionTranscriptDetailspredictionTranscriptInRangepredictionTranscriptToPredictionExonpredictionTranscriptToProbesetprobeDetailsprobeInRangeprobesetDetailsprobesetInRangeprobesetToCdnatranscriptprobesetToDomainprobesetToEstExonprobesetToEstGeneprobesetToEstTranscriptprobesetToExonprobesetToGeneprobesetToHitprobesetToPredictionTranscriptprobesetToProbeprobesetToProteinprobesetToTranscriptprobeToHitprobeToProbesetproteinCoordsToGenomeproteinDetailsproteinInRangeproteinToDomainproteinToGeneproteinToProbesetproteinToTranscriptseqnameMappingseqnamesToEnsemblseqnamesToNCBIspliceGroupIndexspliceIndexstrandAsIntegersymbolToEstGenesymbolToEstTranscriptsymbolToGenesymbolToTranscriptsynonymDetailssynonymToEstGenesynonymToEstTranscriptsynonymToGenesynonymToTranscripttranscriptCoordsToGenometranscriptDetailstranscriptInRangetranscriptToCdnaprobesettranscriptToCodingExontranscriptToCodingRangetranscriptToDomaintranscriptToExontranscriptToExonProbesettranscriptToGenetranscriptToProbesettranscriptToProteintranscriptToSynonymtranscriptToTranslatedprobestranscriptToUtrExontranscriptToUtrRangeunreliableutrProbesets
Dependencies:annotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdigestfastmapformatRfutile.loggerfutile.optionsgenefilterGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RhtslibrlangRMySQLRsamtoolsRSQLiteS4VectorssnowsurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Provide access to the Annmap annotation database | annmap-package annmap |
| annmap 'all' functions | allArrays allChromosomes allDomains allEstExons allEstGenes allEstTranscripts allExons allGenes allPredictionTranscripts allProbes allProbesets allProteins allSymbols allSynonyms allTranscripts annmapAll |
| annmap co-ordinate mapping functions | genomeToProteinCoords genomeToTranscriptCoords proteinCoordsToGenome transcriptCoordsToGenome |
| annmap 'details' functions | annmapDetails arrayDetails chromosomeDetails domainDetails estExonDetails estGeneDetails estTranscriptDetails exonDetails geneDetails predictionTranscriptDetails probeDetails probesetDetails proteinDetails synonymDetails transcriptDetails |
| annmap 'env' functions | annmapEnv annmapGetParam annmapSetParam |
| annmap 'filter' functions | annmapFilters exonic hasProbes hasProbesAtleast hasProbesBetween hasProbesIn intergenic intronic isExonic isIntergenic isIntronic isUnreliable unreliable |
| annmap 'range' functions | 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 |
| Seqnames manipulation functions | annmapSeqname generalisedNameToEnsembl generalisedNameToNCBI seqnameMapping seqnamesToEnsembl seqnamesToNCBI |
| annmap 'to' functions | 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 |
| annmap 'utils' functions | annmapAddConnection annmapClearCache annmapConnect annmapDisconnect annmapGenePlot annmapRangeApply annmapToggleCaching annmapUtils arrayType geneToGeneRegionTrack strandAsInteger |
| annmap coding functions | codingProbesets nonIntronicGeneLength nonIntronicTranscriptLength transcriptToCodingExon transcriptToCodingRange transcriptToUtrExon transcriptToUtrRange utrProbesets |
| Plotting a section of a chromosome. | genomicExonDepthPlot genomicPlot genomicProbePlot |
| Plotting BAM file data alongside the features of a chromosome | convertBamToRle generateBridgeData ngsBridgePlot ngsTraceLabel ngsTracePlotter ngsTraceScale |
| Splice indexing | spliceGroupIndex spliceIndex |