annmap-package | Provide access to the Annmap annotation database |
allArrays | annmap 'all' functions |
allChromosomes | annmap 'all' functions |
allDomains | annmap 'all' functions |
allEstExons | annmap 'all' functions |
allEstGenes | annmap 'all' functions |
allEstTranscripts | annmap 'all' functions |
allExons | annmap 'all' functions |
allGenes | annmap 'all' functions |
allPredictionTranscripts | annmap 'all' functions |
allProbes | annmap 'all' functions |
allProbesets | annmap 'all' functions |
allProteins | annmap 'all' functions |
allSymbols | annmap 'all' functions |
allSynonyms | annmap 'all' functions |
allTranscripts | annmap 'all' functions |
annmap | Provide access to the Annmap annotation database |
annmapAddConnection | annmap 'utils' functions |
annmapAll | annmap 'all' functions |
annmapClearCache | annmap 'utils' functions |
annmapConnect | annmap 'utils' functions |
annmapDetails | annmap 'details' functions |
annmapDisconnect | annmap 'utils' functions |
annmapEnv | annmap 'env' functions |
annmapFilters | annmap 'filter' functions |
annmapGenePlot | annmap 'utils' functions |
annmapGetParam | annmap 'env' functions |
annmapRange | annmap 'range' functions |
annmapRangeApply | annmap 'utils' functions |
annmapSeqname | Seqnames manipulation functions |
annmapSetParam | annmap 'env' functions |
annmapTo | annmap 'to' functions |
annmapToggleCaching | annmap 'utils' functions |
annmapUtils | annmap 'utils' functions |
arrayDetails | annmap 'details' functions |
arrayToProbeset | annmap 'to' functions |
arrayType | annmap 'utils' functions |
chromosomeDetails | annmap 'details' functions |
codingProbesets | annmap coding functions |
convertBamToRle | Plotting BAM file data alongside the features of a chromosome |
domainDetails | annmap 'details' functions |
domainInRange | annmap 'range' functions |
domainInRange-method | annmap 'range' functions |
domainToGene | annmap 'to' functions |
domainToProbeset | annmap 'to' functions |
domainToProtein | annmap 'to' functions |
domainToTranscript | annmap 'to' functions |
estExonDetails | annmap 'details' functions |
estExonInRange | annmap 'range' functions |
estExonInRange-method | annmap 'range' functions |
estExonToEstGene | annmap 'to' functions |
estExonToEstTranscript | annmap 'to' functions |
estExonToProbeset | annmap 'to' functions |
estGeneDetails | annmap 'details' functions |
estGeneInRange | annmap 'range' functions |
estGeneInRange-method | annmap 'range' functions |
estGeneToEstExon | annmap 'to' functions |
estGeneToEstTranscript | annmap 'to' functions |
estGeneToProbeset | annmap 'to' functions |
estTranscriptDetails | annmap 'details' functions |
estTranscriptInRange | annmap 'range' functions |
estTranscriptInRange-method | annmap 'range' functions |
estTranscriptToEstExon | annmap 'to' functions |
estTranscriptToEstGene | annmap 'to' functions |
estTranscriptToProbeset | annmap 'to' functions |
exonDetails | annmap 'details' functions |
exonic | annmap 'filter' functions |
exonInRange | annmap 'range' functions |
exonInRange-method | annmap 'range' functions |
exonToGene | annmap 'to' functions |
exonToProbeset | annmap 'to' functions |
exonToTranscript | annmap 'to' functions |
geneDetails | annmap 'details' functions |
geneInRange | annmap 'range' functions |
geneInRange-method | annmap 'range' functions |
generalisedNameToEnsembl | Seqnames manipulation functions |
generalisedNameToNCBI | Seqnames manipulation functions |
generateBridgeData | Plotting BAM file data alongside the features of a chromosome |
geneToDomain | annmap 'to' functions |
geneToExon | annmap 'to' functions |
geneToExonProbeset | annmap 'to' functions |
geneToExonProbesetExpr | annmap 'to' functions |
geneToGeneRegionTrack | annmap 'utils' functions |
geneToProbeset | annmap 'to' functions |
geneToProtein | annmap 'to' functions |
geneToSymbol | annmap 'to' functions |
geneToSynonym | annmap 'to' functions |
geneToTranscript | annmap 'to' functions |
genomeToProteinCoords | annmap co-ordinate mapping functions |
genomeToTranscriptCoords | annmap co-ordinate mapping functions |
genomicExonDepthPlot | Plotting a section of a chromosome. |
genomicPlot | Plotting a section of a chromosome. |
genomicProbePlot | Plotting a section of a chromosome. |
hasProbes | annmap 'filter' functions |
hasProbesAtleast | annmap 'filter' functions |
hasProbesBetween | annmap 'filter' functions |
hasProbesIn | annmap 'filter' functions |
intergenic | annmap 'filter' functions |
intronic | annmap 'filter' functions |
isExonic | annmap 'filter' functions |
isIntergenic | annmap 'filter' functions |
isIntronic | annmap 'filter' functions |
isUnreliable | annmap 'filter' functions |
ngsBridgePlot | Plotting BAM file data alongside the features of a chromosome |
ngsTraceLabel | Plotting BAM file data alongside the features of a chromosome |
ngsTracePlotter | Plotting BAM file data alongside the features of a chromosome |
ngsTraceScale | Plotting BAM file data alongside the features of a chromosome |
nonIntronicGeneLength | annmap coding functions |
nonIntronicTranscriptLength | annmap coding functions |
predictionTranscriptDetails | annmap 'details' functions |
predictionTranscriptInRange | annmap 'range' functions |
predictionTranscriptInRange-method | annmap 'range' functions |
predictionTranscriptToPredictionExon | annmap 'to' functions |
predictionTranscriptToProbeset | annmap 'to' functions |
probeDetails | annmap 'details' functions |
probeInRange | annmap 'range' functions |
probeInRange-method | annmap 'range' functions |
probesetDetails | annmap 'details' functions |
probesetInRange | annmap 'range' functions |
probesetInRange-method | annmap 'range' functions |
probesetToCdnatranscript | annmap 'to' functions |
probesetToDomain | annmap 'to' functions |
probesetToEstExon | annmap 'to' functions |
probesetToEstGene | annmap 'to' functions |
probesetToEstTranscript | annmap 'to' functions |
probesetToExon | annmap 'to' functions |
probesetToGene | annmap 'to' functions |
probesetToHit | annmap 'to' functions |
probesetToPredictionTranscript | annmap 'to' functions |
probesetToProbe | annmap 'to' functions |
probesetToProtein | annmap 'to' functions |
probesetToTranscript | annmap 'to' functions |
probeToHit | annmap 'to' functions |
probeToProbeset | annmap 'to' functions |
proteinCoordsToGenome | annmap co-ordinate mapping functions |
proteinDetails | annmap 'details' functions |
proteinInRange | annmap 'range' functions |
proteinInRange-method | annmap 'range' functions |
proteinToDomain | annmap 'to' functions |
proteinToGene | annmap 'to' functions |
proteinToProbeset | annmap 'to' functions |
proteinToTranscript | annmap 'to' functions |
seqnameMapping | Seqnames manipulation functions |
seqnamesToEnsembl | Seqnames manipulation functions |
seqnamesToNCBI | Seqnames manipulation functions |
spliceGroupIndex | Splice indexing |
spliceIndex | Splice indexing |
strandAsInteger | annmap 'utils' functions |
symbolToEstGene | annmap 'to' functions |
symbolToEstTranscript | annmap 'to' functions |
symbolToGene | annmap 'to' functions |
symbolToTranscript | annmap 'to' functions |
synonymDetails | annmap 'details' functions |
synonymToEstGene | annmap 'to' functions |
synonymToEstTranscript | annmap 'to' functions |
synonymToGene | annmap 'to' functions |
synonymToTranscript | annmap 'to' functions |
transcriptCoordsToGenome | annmap co-ordinate mapping functions |
transcriptDetails | annmap 'details' functions |
transcriptInRange | annmap 'range' functions |
transcriptInRange-method | annmap 'range' functions |
transcriptToCdnaprobeset | annmap 'to' functions |
transcriptToCodingExon | annmap coding functions |
transcriptToCodingRange | annmap coding functions |
transcriptToDomain | annmap 'to' functions |
transcriptToExon | annmap 'to' functions |
transcriptToExonProbeset | annmap 'to' functions |
transcriptToGene | annmap 'to' functions |
transcriptToProbeset | annmap 'to' functions |
transcriptToProtein | annmap 'to' functions |
transcriptToSynonym | annmap 'to' functions |
transcriptToTranslatedprobes | annmap 'to' functions |
transcriptToUtrExon | annmap coding functions |
transcriptToUtrRange | annmap coding functions |
unreliable | annmap 'filter' functions |
utrProbesets | annmap coding functions |