annmap
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Package index
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Vignettes
Functions
448
Source code
29
Man pages
14
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annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
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API

API for annmap
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Global functions
.attr Source code
.build.sql2 Source code
.cache.exists Source code
.cache.retrieve Source code
.cache.store Source code
.coerce Source code
.data.frame.to.rangeddata Source code
.debug.full Source code
.debug.none Source code
.draw.background.arrow Source code
.draw.genes Source code
.draw.strand Source code
.drop.partial.genes Source code
.duplicate.hash Source code
.fetch.genes.for.range Source code
.filter.whatever Source code
.generate.stats.bits Source code
.genome.to.single.transcript.coords Source code
.get.connection Source code
.get.correct.column Source code
.get.stats.cache Source code
.get.user.string Source code
.has.data Source code
.initialise Source code
.layout.genes Source code
.load.and.parse Source code
.make.hash Source code Source code
.make.params Source code
.needs.array Source code
.nonIntronicLength Source code
.onLoad Source code
.path.for.key Source code
.pretty.size Source code
.probeset.filtering Source code
.process Source code
.range.call Source code
.read.databases Source code
.score.filter Source code
.secret.encoder Source code
.set.cache.root Source code
.set.conf.dir Source code
.single.genome.to.protein.coords Source code
.single.protein.coords.to.genome Source code
.single.transcript.coords.to.genome Source code
.single.transcript.to.utr.range Source code
.usegranges Source code
.ws.make.params Source code
.xmc.all Source code
.xmc.connect Source code
.xmc.db.call Source code
.xmc.db.cleanup Source code
.xmc.details Source code
.xmc.disconnect Source code
.xmc.range Source code
.xmc.to Source code
.xmcws.all Source code
.xmcws.connect Source code
.xmcws.details Source code
.xmcws.disconnect Source code
.xmcws.range Source code
.xmcws.to Source code
allArrays Man page Source code
allChromosomes Man page Source code
allDomains Man page Source code
allEstExons Man page Source code
allEstGenes Man page Source code
allEstTranscripts Man page Source code
allExons Man page Source code
allGenes Man page Source code
allPredictionTranscripts Man page Source code
allProbes Man page Source code
allProbesets Man page Source code
allProteins Man page Source code
allSymbols Man page Source code
allSynonyms Man page Source code
allTranscripts Man page Source code
annmap Man page
annmap-package Man page
annmapAddConnection Man page Source code
annmapAll Man page
annmapClearCache Man page Source code
annmapConnect Man page Source code
annmapDetails Man page
annmapDisconnect Man page Source code
annmapEnv Man page Source code
annmapFilters Man page
annmapGenePlot Man page
annmapGetParam Man page Source code
annmapRange Man page
annmapRangeApply Man page Source code
annmapSeqname Man page
annmapSetParam Man page Source code
annmapTo Man page
annmapToggleCaching Man page Source code
annmapUtils Man page
arrayDetails Man page Source code
arrayToProbeset Man page Source code
arrayType Man page Source code
chromosomeDetails Man page Source code
codingProbesets Man page Source code
convertBamToRle Man page Source code
domainDetails Man page Source code
domainInRange Man page Source code
domainInRange,GRanges-method Man page
domainInRange,NULL-method Man page
domainInRange,RangedData-method Man page
domainInRange,character-method Man page
domainInRange,data.frame-method Man page
domainInRange,factor-method Man page
domainToGene Man page Source code
domainToProbeset Man page Source code
domainToProtein Man page Source code
domainToTranscript Man page Source code
estExonDetails Man page Source code
estExonInRange Man page Source code
estExonInRange,GRanges-method Man page
estExonInRange,NULL-method Man page
estExonInRange,RangedData-method Man page
estExonInRange,character-method Man page
estExonInRange,data.frame-method Man page
estExonInRange,factor-method Man page
estExonToEstGene Man page Source code
estExonToEstTranscript Man page Source code
estExonToProbeset Man page Source code
estGeneDetails Man page Source code
estGeneInRange Man page Source code
estGeneInRange,GRanges-method Man page
estGeneInRange,NULL-method Man page
estGeneInRange,RangedData-method Man page
estGeneInRange,character-method Man page
estGeneInRange,data.frame-method Man page
estGeneInRange,factor-method Man page
estGeneToEstExon Man page Source code
estGeneToEstTranscript Man page Source code
estGeneToProbeset Man page Source code
estTranscriptDetails Man page Source code
estTranscriptInRange Man page Source code
estTranscriptInRange,GRanges-method Man page
estTranscriptInRange,NULL-method Man page
estTranscriptInRange,RangedData-method Man page
estTranscriptInRange,character-method Man page
estTranscriptInRange,data.frame-method Man page
estTranscriptInRange,factor-method Man page
estTranscriptToEstExon Man page Source code
estTranscriptToEstGene Man page Source code
estTranscriptToProbeset Man page Source code
exonDetails Man page Source code
exonInRange Man page Source code
exonInRange,GRanges-method Man page
exonInRange,NULL-method Man page
exonInRange,RangedData-method Man page
exonInRange,character-method Man page
exonInRange,data.frame-method Man page
exonInRange,factor-method Man page
exonToGene Man page Source code
exonToProbeset Man page Source code
exonToTranscript Man page Source code
exonic Man page Source code
geneDetails Man page Source code
geneInRange Man page Source code
geneInRange,GRanges-method Man page
geneInRange,NULL-method Man page
geneInRange,RangedData-method Man page
geneInRange,character-method Man page
geneInRange,data.frame-method Man page
geneInRange,factor-method Man page
geneToDomain Man page Source code
geneToExon Man page Source code
geneToExonProbeset Man page Source code
geneToExonProbesetExpr Man page Source code
geneToGeneRegionTrack Man page Source code
geneToProbeset Man page Source code
geneToProtein Man page Source code
geneToSymbol Man page Source code
geneToSynonym Man page Source code
geneToTranscript Man page Source code
generalisedNameToEnsembl Man page Source code
generalisedNameToNCBI Man page Source code
generateBridgeData Man page Source code
genomeToProteinCoords Man page Source code
genomeToTranscriptCoords Man page Source code
genomicExonDepthPlot Man page Source code
genomicPlot Man page Source code
genomicProbePlot Man page Source code
hasProbes Man page Source code
hasProbesAtleast Man page Source code
hasProbesBetween Man page Source code
hasProbesIn Man page Source code
intergenic Man page Source code
intronic Man page Source code
isExonic Man page Source code
isIntergenic Man page Source code
isIntronic Man page Source code
isUnreliable Man page Source code
ngsBridgePlot Man page Source code
ngsTraceLabel Man page Source code
ngsTracePlotter Man page Source code
ngsTraceScale Man page Source code
nonIntronicGeneLength Man page Source code
nonIntronicTranscriptLength Man page Source code
predictionTranscriptDetails Man page Source code
predictionTranscriptInRange Man page Source code
predictionTranscriptInRange,GRanges-method Man page
predictionTranscriptInRange,NULL-method Man page
predictionTranscriptInRange,RangedData-method Man page
predictionTranscriptInRange,character-method Man page
predictionTranscriptInRange,data.frame-method Man page
predictionTranscriptInRange,factor-method Man page
predictionTranscriptToPredictionExon Man page Source code
predictionTranscriptToProbeset Man page Source code
probeDetails Man page Source code
probeInRange Man page Source code
probeInRange,GRanges-method Man page
probeInRange,NULL-method Man page
probeInRange,RangedData-method Man page
probeInRange,character-method Man page
probeInRange,data.frame-method Man page
probeInRange,factor-method Man page
probeToHit Man page Source code
probeToProbeset Man page Source code
probesetDetails Man page Source code
probesetInRange Man page Source code
probesetInRange,GRanges-method Man page
probesetInRange,NULL-method Man page
probesetInRange,RangedData-method Man page
probesetInRange,character-method Man page
probesetInRange,data.frame-method Man page
probesetInRange,factor-method Man page
probesetToCdnatranscript Man page Source code
probesetToDomain Man page Source code
probesetToEstExon Man page Source code
probesetToEstGene Man page Source code
probesetToEstTranscript Man page Source code
probesetToExon Man page Source code
probesetToGene Man page Source code
probesetToHit Man page Source code
probesetToPredictionTranscript Man page Source code
probesetToProbe Man page Source code
probesetToProtein Man page Source code
probesetToTranscript Man page Source code
proteinCoordsToGenome Man page Source code
proteinDetails Man page Source code
proteinInRange Man page Source code
proteinInRange,GRanges-method Man page
proteinInRange,NULL-method Man page
proteinInRange,RangedData-method Man page
proteinInRange,character-method Man page
proteinInRange,data.frame-method Man page
proteinInRange,factor-method Man page
proteinToDomain Man page Source code
proteinToGene Man page Source code
proteinToProbeset Man page Source code
proteinToTranscript Man page Source code
seqnameMapping Man page Source code
seqnamesToEnsembl Man page Source code
seqnamesToNCBI Man page Source code
spliceGroupIndex Man page Source code
spliceIndex Man page Source code
strandAsInteger Man page Source code
symbolToEstGene Man page Source code
symbolToEstTranscript Man page Source code
symbolToGene Man page Source code
symbolToTranscript Man page Source code
synonymDetails Man page Source code
synonymToEstGene Man page Source code
synonymToEstTranscript Man page Source code
synonymToGene Man page Source code
synonymToTranscript Man page Source code
transcriptCoordsToGenome Man page Source code
transcriptDetails Man page Source code
transcriptInRange Man page Source code
transcriptInRange,GRanges-method Man page
transcriptInRange,NULL-method Man page
transcriptInRange,RangedData-method Man page
transcriptInRange,character-method Man page
transcriptInRange,data.frame-method Man page
transcriptInRange,factor-method Man page
transcriptToCdnaprobeset Man page Source code
transcriptToCodingExon Man page Source code
transcriptToCodingRange Man page Source code
transcriptToDomain Man page Source code
transcriptToExon Man page Source code
transcriptToExonProbeset Man page Source code
transcriptToGene Man page Source code
transcriptToProbeset Man page Source code
transcriptToProtein Man page Source code
transcriptToSynonym Man page Source code
transcriptToTranslatedprobes Man page Source code
transcriptToUtrExon Man page Source code
transcriptToUtrRange Man page Source code
unreliable Man page Source code
utrProbesets Man page Source code
annmap documentation built on Nov. 8, 2020, 7:43 p.m.

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