bamSummarise	bamSummarise
bamSummariseByChr	bamSummariseByChr
bamSummaryToCoverage	bamSummaryToCoverage
cas9CoverageTypeOverChromosomes	cas9CoverageTypeOverChromosomes
cas9ExecutiveSummary	cas9ExecutiveSummary
cas9GetTargetList	cas9GetTargetList
cas9MappingByGenomicSegment	cas9MappingByGenomicSegment
cas9MultiGeneCoveragePanel	cas9MultiGeneCoveragePanel
cas9OffTargetKaryogram	cas9OffTargetKaryogram
cas9OffTargetTable	cas9OffTargetTable
cas9SingleTargetPlot	cas9SingleTargetPlot
cas9StrandedTargetPlot	cas9StrandedTargetPlot
cas9TargetPerformanceTable	cas9TargetPerformanceTable
cas9WriteExcelOffTarget	cas9WriteExcelOffTarget
cas9WriteExcelOnTarget	cas9WriteExcelOnTarget
chromosomeMappingSummary	chromosomeMappingSummary
cleanReferenceGenome	cleanReferenceGenome
fastqCheckup	fastqCheckup
fastqValidator	fastqValidator
fixFastq	fixFastq
getChromosomeIds	getChromosomeIds
getChromosomeSequence	getChromosomeSequence
getFastqBases	getFastqBases
getFastqCount	getFastqCount
getFastqPlusErrorCount	getFastqPlusErrorCount
getFlongleChannelMap	getFlongleChannelMap
getMalformedFastqHeaderCount	getMalformedFastqHeaderCount
getMinIONChannelMap	getMinIONChannelMap
getOutputFormat	getOutputFormat
getPlotDimensions	getPlotDimensions
getReferenceGenome	getReferenceGenome
getRpath	getRpath
getSeqLengths	getSeqLengths
getSequenceQualityMismatchCount	getSequenceQualityMismatchCount
getSkippedLineCount	getSkippedLineCount
getStringSetId	getStringSetId
getZeroLengthSequenceCount	getZeroLengthSequenceCount
ggbiosave	ggbiosave
importCas9TutorialData	importCas9TutorialData
importSequencingSummary	importSequencingSummary
infoGraphicPlot3	infoGraphicPlot3
infoGraphicPlot4	infoGraphicPlot4
infoGraphicPlot5	infoGraphicPlot5
init	init
isInitialised	isInitialised
lcalc	lcalc
LeftRightPlot	LeftRightPlot
listCachedObjects	listCachedObjects
listOutputFormat	listOutputFormat
loadReferenceGenome	loadReferenceGenome
md5sum	md5sum
ncalc	ncalc
parallelBamSummarise	parallelBamSummarise
phredmean	phredmean
plotAlignmentAccuracy	plotAlignmentAccuracy
plotAlignmentIdentity	plotAlignmentIdentity
plotDepthOfCoverageMegablock	plotDepthOfCoverageMegablock
plotOverallCovHistogram	plotOverallCovHistogram
qualToMeanQ	qualToMeanQ
RepeatMaskerGR	RepeatMaskerGR
SequenceSummaryBarcodeHistogram	SequenceSummaryBarcodeHistogram
SequenceSummaryBarcodeInfoGraphic	SequenceSummaryBarcodeInfoGraphic
SequenceSummaryBarcodeTable	SequenceSummaryBarcodeTable
SequenceSummaryBasicInfoPlot	SequenceSummaryBasicInfoPlot
SequenceSummaryExecutiveSummary	SequenceSummaryExecutiveSummary
SequencingSummaryActiveChannelPlot	SequencingSummaryActiveChannelPlot
SequencingSummaryBarcodeMerge	SequencingSummaryBarcodeMerge
SequencingSummaryBase50	SequencingSummaryBase50
SequencingSummaryChannelActivity	SequencingSummaryChannelActivity
SequencingSummaryCumulativeBases	SequencingSummaryCumulativeBases
SequencingSummaryCumulativeReads	SequencingSummaryCumulativeReads
SequencingSummaryGetPlatform	SequencingSummaryGetPlatform
SequencingSummaryPassGauge	SequencingSummaryPassGauge
SequencingSummaryReadLengthHistogram	SequencingSummaryReadLengthHistogram
SequencingSummaryReadLengthQualityDensity	SequencingSummaryReadLengthQualityDensity
SequencingSummaryReadQualityHistogram	SequencingSummaryReadQualityHistogram
SequencingSummarySpeedPlot	SequencingSummarySpeedPlot
SequencingSummaryT50	SequencingSummaryT50
SequencingSummaryTemporalThroughput	SequencingSummaryTemporalThroughput
SequencingSummaryWeightedReadLength	SequencingSummaryWeightedReadLength
setLogFile	setLogFile
setOutputFormat	setOutputFormat
setPlotDimensions	setPlotDimensions
setReferenceGenome	setReferenceGenome
setRpath	setRpath
snifflesKaryogram	snifflesKaryogram
sourceCas9Parameters	sourceCas9Parameters
svLengthDistribution	svLengthDistribution
SVMappingCharacteristicTable	SVMappingCharacteristicTable
testBam	testBam
unsetLog	unsetLog
Vcf2FilteredGranges	Vcf2FilteredGranges
Vcf2GRanges	Vcf2GRanges
