.addPercent	dot-addPercent
.emptyPlot	dot-emptyPlot
.FastqcFile-class	dot-FastqcFile-class
.getToolName	dot-getToolName
.hidePWFRects	dot-hidePWFRects
.isValidAdapterRemovalLog	dot-isValidAdapterRemovalLog
.isValidBowtieLog	dot-isValidBowtieLog
.isValidBuscoLog	dot-isValidBuscoLog
.isValidCutadaptLog	dot-isValidCutadaptLog
.isValidDuplicationMetricsLog	dot-isValidDuplicationMetricsLog
.isValidFeatureCountsLog	dot-isValidFeatureCountsLog
.isValidFlagstatLog	dot-isValidFlagstatLog
.isValidHisat2Log	dot-isValidHisat2Log
.isValidQuastLog	dot-isValidQuastLog
.isValidStarLog	dot-isValidStarLog
.isValidTrimmomaticLog	dot-isValidTrimmomaticLog
.makeDendro	dot-makeDendro
.makeLabels	dot-makeLabels
.makeSidebar	dot-makeSidebar
.parseAdapterRemovalLogs	dot-parseAdapterRemovalLogs
.parseBowtieLogs	dot-parseBowtieLogs
.parseBuscoLogs	dot-parseBuscoLogs
.parseCutadaptLogs	dot-parseCutadaptLogs
.parseDuplicationMetricsLogs	dot-parseDuplicationMetricsLogs
.parseFeatureCountsLogs	dot-parseFeatureCountsLogs
.parseFlagstatLogs	dot-parseFlagstatLogs
.parseHisat2Logs	dot-parseHisat2Logs
.parseQuastLogs	dot-parseQuastLogs
.parseStarLogs	dot-parseStarLogs
.parseTrimmomaticLogs	dot-parseTrimmomaticLogs
.renderDendro	dot-renderDendro
.scale_fill_pwf	dot-scale_fill_pwf
.splitByTab	dot-splitByTab
estGcDistn	estGcDistn
estGcDistn,ANY-method	estGcDistn
estGcDistn,character-method	estGcDistn
estGcDistn,DNAStringSet-method	estGcDistn
FastqcData	FastqcData
FastqcData-class	FastqcData
FastqcDataList	FastqcDataList
FastqcDataList-class	FastqcDataList
fqcVersion	fqcVersion
fqcVersion,ANY-method	fqcVersion
fqcVersion,FastqcData-method	fqcVersion
fqcVersion,FastqcDataList-method	fqcVersion
fqName	fqName-methods
fqName,ANY-method	fqName-methods
fqName,FastqcData-method	fqName-methods
fqName,FastqcDataList-method	fqName-methods
gcAvail	gcAvail
gcAvail,TheoreticalGC-method	gcAvail
gcTheoretical	gcTheoretical
getColours	getColours-methods
getColours,PwfCols-method	getColours-methods
getGC	getGC
getGC,ANY-method	getGC
getGC,TheoreticalGC-method	getGC
getModule	getModule
getModule,ANY-method	getModule
getModule,FastqcData-method	getModule
getModule,FastqcDataList-method	getModule
getSummary	getSummary
getSummary,.FastqcFile-method	getSummary
getSummary,ANY-method	getSummary
getSummary,FastqcData-method	getSummary
getSummary,FastqcDataList-method	getSummary
importNgsLogs	importNgsLogs
importSJ	importSJ
isCompressed	isCompressed
maxAdapterContent	maxAdapterContent
mData	mData
mData,TheoreticalGC-method	mData
overRep2Fasta	overRep2Fasta-methods
overRep2Fasta,ANY-method	overRep2Fasta-methods
overRep2Fasta,FastqcData-method	overRep2Fasta-methods
overRep2Fasta,FastqcDataList-method	overRep2Fasta-methods
path	path
path,.FastqcFile-method	path
path,FastqcData-method	path
path,FastqcDataList-method	path
plotAdapterContent	plotAdapterContent-methods
plotAdapterContent,ANY-method	plotAdapterContent-methods
plotAdapterContent,character-method	plotAdapterContent-methods
plotAdapterContent,FastqcData-method	plotAdapterContent-methods
plotAdapterContent,FastqcDataList-method	plotAdapterContent-methods
plotAlignmentSummary	plotAlignmentSummary
plotAssemblyStats	plotAssemblyStats
plotBaseQuals	plotBaseQuals-methods
plotBaseQuals,ANY-method	plotBaseQuals-methods
plotBaseQuals,character-method	plotBaseQuals-methods
plotBaseQuals,FastqcData-method	plotBaseQuals-methods
plotBaseQuals,FastqcDataList-method	plotBaseQuals-methods
plotDupLevels	plotDupLevels-methods
plotDupLevels,ANY-method	plotDupLevels-methods
plotDupLevels,character-method	plotDupLevels-methods
plotDupLevels,FastqcData-method	plotDupLevels-methods
plotDupLevels,FastqcDataList-method	plotDupLevels-methods
plotFastqcPCA	plotFastqcPCA-methods
plotFastqcPCA,ANY-method	plotFastqcPCA-methods
plotFastqcPCA,character-method	plotFastqcPCA-methods
plotFastqcPCA,FastqcDataList-method	plotFastqcPCA-methods
plotGcContent	plotGcContent-methods
plotGcContent,ANY-method	plotGcContent-methods
plotGcContent,character-method	plotGcContent-methods
plotGcContent,FastqcData-method	plotGcContent-methods
plotGcContent,FastqcDataList-method	plotGcContent-methods
plotKmers	plotKmers-methods
plotKmers,ANY-method	plotKmers-methods
plotKmers,character-method	plotKmers-methods
plotKmers,FastqcData-method	plotKmers-methods
plotKmers,FastqcDataList-method	plotKmers-methods
plotNContent	plotNContent-methods
plotNContent,ANY-method	plotNContent-methods
plotNContent,character-method	plotNContent-methods
plotNContent,FastqcData-method	plotNContent-methods
plotNContent,FastqcDataList-method	plotNContent-methods
plotOverrep	plotOverrep-methods
plotOverrep,ANY-method	plotOverrep-methods
plotOverrep,character-method	plotOverrep-methods
plotOverrep,FastqcData-method	plotOverrep-methods
plotOverrep,FastqcDataList-method	plotOverrep-methods
plotReadTotals	plotReadTotals-methods
plotReadTotals,ANY-method	plotReadTotals-methods
plotReadTotals,character-method	plotReadTotals-methods
plotReadTotals,FastqcDataList-method	plotReadTotals-methods
plotSeqContent	plotSeqContent-methods
plotSeqContent,ANY-method	plotSeqContent-methods
plotSeqContent,character-method	plotSeqContent-methods
plotSeqContent,FastqcData-method	plotSeqContent-methods
plotSeqContent,FastqcDataList-method	plotSeqContent-methods
plotSeqLengthDistn	plotSeqLengthDistn-methods
plotSeqLengthDistn,ANY-method	plotSeqLengthDistn-methods
plotSeqLengthDistn,character-method	plotSeqLengthDistn-methods
plotSeqLengthDistn,FastqcData-method	plotSeqLengthDistn-methods
plotSeqLengthDistn,FastqcDataList-method	plotSeqLengthDistn-methods
plotSeqQuals	plotSeqQuals-methods
plotSeqQuals,ANY-method	plotSeqQuals-methods
plotSeqQuals,character-method	plotSeqQuals-methods
plotSeqQuals,FastqcData-method	plotSeqQuals-methods
plotSeqQuals,FastqcDataList-method	plotSeqQuals-methods
plotSummary	plotSummary-methods
plotSummary,ANY-method	plotSummary-methods
plotSummary,character-method	plotSummary-methods
plotSummary,FastqcDataList-method	plotSummary-methods
pwf	pwf
PwfCols	PwfCols-class
PwfCols-class	PwfCols-class
readTotals	readTotals
runFastQC	runFastQC-methods
runFastQC,ANY-method	runFastQC-methods
runFastQC,BamFile-method	runFastQC-methods
runFastQC,BamFileList-method	runFastQC-methods
runFastQC,FastqFile-method	runFastQC-methods
runFastQC,FastqFileList-method	runFastQC-methods
setAlpha	getColours-methods
setAlpha,PwfCols-method	getColours-methods
setColours	getColours-methods
setColours,PwfCols-method	getColours-methods
TheoreticalGC-class	TheoreticalGC-class
writeHtmlReport	writeHtmlReport
[	extract-methods
[,FastqcDataList,ANY,missing,ANY-method	extract-methods
[,FastqcDataList,character,missing,ANY-method	extract-methods
[,FastqcDataList,logical,missing,ANY-method	extract-methods
[,FastqcDataList,numeric,missing,ANY-method	extract-methods
